diff --git a/.buildkite/test-pipeline.yaml b/.buildkite/test-pipeline.yaml
index b12bf7b382d0..f678436dd05e 100644
--- a/.buildkite/test-pipeline.yaml
+++ b/.buildkite/test-pipeline.yaml
@@ -208,7 +208,7 @@ steps:
   - tests/spec_decode
   commands:
     - pytest -v -s spec_decode/e2e/test_multistep_correctness.py
-    - pytest -v -s spec_decode --ignore=spec_decode/e2e/test_multistep_correctness.py
+    - VLLM_ATTENTION_BACKEND=FLASH_ATTN pytest -v -s spec_decode --ignore=spec_decode/e2e/test_multistep_correctness.py
 
 - label: LoRA Test %N # 15min each
   mirror_hardwares: [amd]
diff --git a/tests/samplers/test_sampler.py b/tests/samplers/test_sampler.py
index 3342a336a4ef..9d4932dd1f5b 100644
--- a/tests/samplers/test_sampler.py
+++ b/tests/samplers/test_sampler.py
@@ -434,7 +434,7 @@ def run_test_case(*, expected_penalization: List[bool],
         sampling_metadata = SamplingMetadata.prepare(
             seq_group_metadata_list,
             seq_lens=seq_lens if seq_lens else None,
-            query_lens=seq_lens if seq_lens else None,
+            query_lens=seq_lens if seq_lens else [1] * batch_size,
             device=device,
             pin_memory=is_pin_memory_available())
         # the logits tensor is modified in-place by the sampler
diff --git a/tests/spec_decode/e2e/test_integration.py b/tests/spec_decode/e2e/test_integration.py
index 4a427d4c3e28..d04e312689bc 100644
--- a/tests/spec_decode/e2e/test_integration.py
+++ b/tests/spec_decode/e2e/test_integration.py
@@ -102,3 +102,47 @@ def test_speculative_model_quantization_config(vllm_runner, common_llm_kwargs,
                                   max_output_len=32,
                                   seed=seed,
                                   temperature=0.0)
+
+
+@pytest.mark.parametrize(
+    "common_llm_kwargs",
+    [{
+        "model_name": MAIN_MODEL,
+
+        # Skip cuda graph recording for fast test.
+        "enforce_eager": True,
+
+        # Required for spec decode.
+        "use_v2_block_manager": True,
+        "speculative_model": "JackFram/llama-68m",
+        "num_speculative_tokens": 3,
+    }])
+@pytest.mark.parametrize("per_test_common_llm_kwargs", [{}])
+@pytest.mark.parametrize("baseline_llm_kwargs", [{}])
+@pytest.mark.parametrize("test_llm_kwargs",
+                         [{
+                             "speculative_disable_mqa_scorer": True,
+                         }])
+@pytest.mark.parametrize("batch_size", [1, 5])
+@pytest.mark.parametrize(
+    "output_len",
+    [
+        # Use smaller output len for fast test.
+        32,
+    ])
+@pytest.mark.parametrize("seed", [1])
+def test_mqa_scorer(vllm_runner, common_llm_kwargs, per_test_common_llm_kwargs,
+                    baseline_llm_kwargs, test_llm_kwargs, batch_size: int,
+                    output_len: int, seed: int):
+    """Verify that ngram speculative decoding generates the same output 
+    with batch expansion scorer and mqa scorer.
+    """
+    run_equality_correctness_test(vllm_runner,
+                                  common_llm_kwargs,
+                                  per_test_common_llm_kwargs,
+                                  baseline_llm_kwargs,
+                                  test_llm_kwargs,
+                                  batch_size,
+                                  max_output_len=output_len,
+                                  seed=seed,
+                                  temperature=0.0)
diff --git a/tests/spec_decode/e2e/test_medusa_correctness.py b/tests/spec_decode/e2e/test_medusa_correctness.py
index 8c90e147df23..0b36e712a11b 100644
--- a/tests/spec_decode/e2e/test_medusa_correctness.py
+++ b/tests/spec_decode/e2e/test_medusa_correctness.py
@@ -350,6 +350,55 @@ def test_medusa_disable_queue(vllm_runner, common_llm_kwargs,
                                   temperature=0.0)
 
 
+@pytest.mark.parametrize(
+    "common_llm_kwargs",
+    [{
+        # Skip cuda graph recording for fast test.
+        "enforce_eager": True,
+
+        # Required for spec decode.
+        "use_v2_block_manager": True,
+
+        # Precision
+        "dtype": PRECISION,
+
+        # Main model
+        "model_name": MAIN_MODEL,
+        "speculative_model": SPEC_MODEL,
+        "num_speculative_tokens": MAX_SPEC_TOKENS,
+        "speculative_disable_by_batch_size": 4
+    }])
+@pytest.mark.parametrize("per_test_common_llm_kwargs", [{}])
+@pytest.mark.parametrize("baseline_llm_kwargs", [{}])
+@pytest.mark.parametrize("test_llm_kwargs",
+                         [{
+                             "speculative_disable_mqa_scorer": True,
+                         }])
+@pytest.mark.parametrize("batch_size", [1, 5])
+@pytest.mark.parametrize(
+    "output_len",
+    [
+        # Use smaller output len for fast test.
+        32,
+    ])
+@pytest.mark.parametrize("seed", [1])
+def test_mqa_scorer(vllm_runner, common_llm_kwargs, per_test_common_llm_kwargs,
+                    baseline_llm_kwargs, test_llm_kwargs, batch_size: int,
+                    output_len: int, seed: int):
+    """Verify that speculative decoding generates the same output 
+    with batch expansion scorer and mqa scorer.
+    """
+    run_equality_correctness_test(vllm_runner,
+                                  common_llm_kwargs,
+                                  per_test_common_llm_kwargs,
+                                  baseline_llm_kwargs,
+                                  test_llm_kwargs,
+                                  batch_size,
+                                  max_output_len=output_len,
+                                  seed=seed,
+                                  temperature=0.0)
+
+
 if __name__ == "__main__":
     import pytest
     pytest.main([__file__])
diff --git a/tests/spec_decode/e2e/test_mlp_correctness.py b/tests/spec_decode/e2e/test_mlp_correctness.py
index 7f3180befaff..52b48a33c309 100644
--- a/tests/spec_decode/e2e/test_mlp_correctness.py
+++ b/tests/spec_decode/e2e/test_mlp_correctness.py
@@ -460,3 +460,46 @@ def test_mlp_disable_queue(vllm_runner, common_llm_kwargs,
                                   max_output_len=output_len,
                                   seed=seed,
                                   temperature=0.0)
+
+
+@pytest.mark.parametrize(
+    "common_llm_kwargs",
+    [{
+        "model_name": MAIN_MODEL,
+
+        # Skip cuda graph recording for fast test.
+        "enforce_eager": True,
+
+        # Required for spec decode.
+        "use_v2_block_manager": True,
+        "speculative_model": SPEC_MODEL,
+    }])
+@pytest.mark.parametrize("per_test_common_llm_kwargs", [{}])
+@pytest.mark.parametrize("baseline_llm_kwargs", [{}])
+@pytest.mark.parametrize("test_llm_kwargs",
+                         [{
+                             "speculative_disable_mqa_scorer": True,
+                         }])
+@pytest.mark.parametrize("batch_size", [1, 5])
+@pytest.mark.parametrize(
+    "output_len",
+    [
+        # Use smaller output len for fast test.
+        32,
+    ])
+@pytest.mark.parametrize("seed", [1])
+def test_mqa_scorer(vllm_runner, common_llm_kwargs, per_test_common_llm_kwargs,
+                    baseline_llm_kwargs, test_llm_kwargs, batch_size: int,
+                    output_len: int, seed: int):
+    """Verify that speculative decoding generates the same output 
+    with batch expansion scorer and mqa scorer.
+    """
+    run_equality_correctness_test(vllm_runner,
+                                  common_llm_kwargs,
+                                  per_test_common_llm_kwargs,
+                                  baseline_llm_kwargs,
+                                  test_llm_kwargs,
+                                  batch_size,
+                                  max_output_len=output_len,
+                                  seed=seed,
+                                  temperature=0.0)
diff --git a/tests/spec_decode/e2e/test_ngram_correctness.py b/tests/spec_decode/e2e/test_ngram_correctness.py
index 850114eb7f5a..586245938316 100644
--- a/tests/spec_decode/e2e/test_ngram_correctness.py
+++ b/tests/spec_decode/e2e/test_ngram_correctness.py
@@ -292,3 +292,49 @@ def test_ngram_disable_queue(vllm_runner, common_llm_kwargs,
                                   max_output_len=output_len,
                                   seed=seed,
                                   temperature=0.0)
+
+
+@pytest.mark.parametrize(
+    "common_llm_kwargs",
+    [{
+        "model_name": "JackFram/llama-68m",
+
+        # Skip cuda graph recording for fast test.
+        "enforce_eager": True,
+
+        # Required for spec decode.
+        "use_v2_block_manager": True,
+        "speculative_model": "[ngram]",
+        "num_speculative_tokens": 5,
+        "ngram_prompt_lookup_max": 3,
+    }])
+@pytest.mark.parametrize("per_test_common_llm_kwargs", [{}])
+@pytest.mark.parametrize("baseline_llm_kwargs", [{}])
+@pytest.mark.parametrize("test_llm_kwargs",
+                         [{
+                             "speculative_disable_mqa_scorer": True,
+                         }])
+@pytest.mark.parametrize("batch_size", [1, 5])
+@pytest.mark.parametrize(
+    "output_len",
+    [
+        # Use smaller output len for fast test.
+        32,
+    ])
+@pytest.mark.parametrize("seed", [1])
+def test_ngram_scorer(vllm_runner, common_llm_kwargs,
+                      per_test_common_llm_kwargs, baseline_llm_kwargs,
+                      test_llm_kwargs, batch_size: int, output_len: int,
+                      seed: int):
+    """Verify that ngram speculative decoding generates the same output 
+    with batch expansion scorer and mqa scorer.
+    """
+    run_equality_correctness_test(vllm_runner,
+                                  common_llm_kwargs,
+                                  per_test_common_llm_kwargs,
+                                  baseline_llm_kwargs,
+                                  test_llm_kwargs,
+                                  batch_size,
+                                  max_output_len=output_len,
+                                  seed=seed,
+                                  temperature=0.0)
diff --git a/tests/spec_decode/test_multi_step_worker.py b/tests/spec_decode/test_multi_step_worker.py
index 6fa386ffab12..e6f7f480eebb 100644
--- a/tests/spec_decode/test_multi_step_worker.py
+++ b/tests/spec_decode/test_multi_step_worker.py
@@ -173,7 +173,6 @@ def test_same_output_for_multi_step():
         block_size,
         num_gpu_blocks,
         seed,
-        model_runner_cls=TP1DraftModelRunner,
     )
 
     worker = create_worker(
diff --git a/tests/spec_decode/test_scorer.py b/tests/spec_decode/test_scorer.py
new file mode 100644
index 000000000000..5f703b03ab7f
--- /dev/null
+++ b/tests/spec_decode/test_scorer.py
@@ -0,0 +1,65 @@
+import pytest
+import torch
+
+from vllm.sequence import ExecuteModelRequest
+from vllm.spec_decode.batch_expansion import BatchExpansionTop1Scorer
+from vllm.spec_decode.interfaces import SpeculativeProposals, SpeculativeScores
+from vllm.spec_decode.mqa_scorer import MQAScorer
+from vllm.worker.worker import Worker
+
+from .utils import create_batch, create_worker
+
+
+def create_proposal(batch_size: int, propose_len: int, vocab_size: int,
+                    device: str) -> SpeculativeProposals:
+    proposal_probs = torch.rand((batch_size, propose_len, vocab_size),
+                                device=device)
+    proposal_token_ids = torch.argmax(proposal_probs, dim=-1)
+    proposal_lens = torch.tensor([propose_len] * batch_size, device=device)
+    return SpeculativeProposals(proposal_token_ids, proposal_probs,
+                                proposal_lens)
+
+
+def assert_score_equal(score1: SpeculativeScores,
+                       score2: SpeculativeScores) -> None:
+    assert torch.allclose(score1.probs, score2.probs)
+    assert torch.allclose(score1.logprobs, score2.logprobs)
+    assert torch.equal(score1.token_ids, score2.token_ids)
+
+
+@pytest.mark.parametrize('model_name', ['facebook/opt-125m'])
+@pytest.mark.parametrize('batch_size', [1, 2, 4, 8, 16])
+@pytest.mark.parametrize('propose_len', [1, 3, 5])
+@pytest.mark.parametrize('device', ['cuda'])
+def test_scoroer(model_name: str, batch_size: int, propose_len: int,
+                 device: str) -> None:
+    """
+    Compare the batch expansion scorer and mqa scorer return the same score
+    """
+    seed = 0
+    block_size = 32
+    num_gpu_blocks = 2048 // block_size
+    scorer_worker = create_worker(Worker, model_name, block_size,
+                                  num_gpu_blocks, seed)
+    scorer_worker.model_runner.model.sampler.include_gpu_probs_tensor = True
+    scorer_worker.model_runner.model.sampler.\
+        should_modify_greedy_probs_inplace = True
+
+    vocab_size = scorer_worker.vocab_size
+    proposals = create_proposal(batch_size, propose_len, vocab_size, device)
+    seq_group_metadatalist, _, _ = create_batch(batch_size,
+                                                propose_len,
+                                                block_size=block_size,
+                                                num_gpu_blocks=num_gpu_blocks)
+    requests = ExecuteModelRequest(seq_group_metadatalist,
+                                   num_lookahead_slots=propose_len)
+
+    batch_expansion_scorer = BatchExpansionTop1Scorer(scorer_worker, device,
+                                                      vocab_size)
+    batch_expansion_score = batch_expansion_scorer.score_proposals(
+        requests, proposals)
+
+    mqa_scorer = MQAScorer(scorer_worker, device, vocab_size)
+    mqa_score = mqa_scorer.score_proposals(requests, proposals)
+
+    assert_score_equal(batch_expansion_score, mqa_score)
diff --git a/tests/spec_decode/test_spec_decode_worker.py b/tests/spec_decode/test_spec_decode_worker.py
index 501d05756e01..e0b7b7d47f1f 100644
--- a/tests/spec_decode/test_spec_decode_worker.py
+++ b/tests/spec_decode/test_spec_decode_worker.py
@@ -63,10 +63,10 @@ def test_correctly_calls_draft_model(k: int, batch_size: int,
 @pytest.mark.parametrize("acceptance_sampler_method",
                          ["rejection_sampler", "typical_acceptance_sampler"])
 @torch.inference_mode()
-def test_correctly_calls_target_model(k: int, batch_size: int,
-                                      acceptance_sampler_method: str):
+def test_batch_expansion_correctly_calls_target_model(
+        k: int, batch_size: int, acceptance_sampler_method: str):
     """Verify SpecDecodeWorker calls the target model with correct
-    inputs. Everything else is mocked out.
+    inputs with batch expansion. Everything else is mocked out.
     """
     draft_worker = mock_worker(cls=MultiStepWorker, use_spec=False)
     target_worker = mock_worker(use_spec=False)
@@ -82,7 +82,8 @@ def test_correctly_calls_target_model(k: int, batch_size: int,
         target_worker,
         mock_spec_decode_sampler(acceptance_sampler_method),
         disable_logprobs=False,
-        metrics_collector=metrics_collector)
+        metrics_collector=metrics_collector,
+        disable_mqa_scorer=True)
     worker.init_device()
 
     vocab_size = 32_000
diff --git a/tests/spec_decode/utils.py b/tests/spec_decode/utils.py
index f17e87288163..f683942a5854 100644
--- a/tests/spec_decode/utils.py
+++ b/tests/spec_decode/utils.py
@@ -131,19 +131,22 @@ def create_seq_group_metadata_from_prompts(
         for i, final_len in enumerate(final_prompt_lens)
     }
 
-    return [
-        SequenceGroupMetadata(
-            request_id=str(i),
-            is_prompt=len(cont_token_ids) == 0,
-            seq_data={
-                i: SequenceData.from_seqs(prompt_token_ids[:],
-                                          cont_token_ids[:]),
-            },
-            sampling_params=SamplingParams(temperature=0.0, ),
-            block_tables={i: block_allocations[i][:]},
-        ) for i, (prompt_token_ids,
-                  cont_token_ids) in enumerate(zip(prompts, continuations))
-    ]
+    seq_grou_metadata_list = []
+    for i, (prompt_token_ids,
+            cont_token_ids) in enumerate(zip(prompts, continuations)):
+        data = SequenceData.from_seqs(prompt_token_ids, cont_token_ids)
+        data.update_num_computed_tokens(
+            len(prompt_token_ids) + len(cont_token_ids) - 1)
+        seq_data = {i: data}
+        seq_grou_metadata_list.append(
+            SequenceGroupMetadata(
+                request_id=str(i),
+                is_prompt=len(cont_token_ids) == 0,
+                seq_data=seq_data,
+                sampling_params=SamplingParams(temperature=0.0),
+                block_tables={i: block_allocations[i][:]},
+            ))
+    return seq_grou_metadata_list
 
 
 def assert_logprobs_dict_allclose(
diff --git a/vllm/attention/backends/blocksparse_attn.py b/vllm/attention/backends/blocksparse_attn.py
index 656cfd124ab4..57ac152d9edb 100644
--- a/vllm/attention/backends/blocksparse_attn.py
+++ b/vllm/attention/backends/blocksparse_attn.py
@@ -186,6 +186,12 @@ class BlocksparseFlashAttentionMetadata(AttentionMetadata):
     # TODO(woosuk): Move `use_cuda_graph` out since it's unrelated to attention.
     use_cuda_graph: bool
 
+    # Number of query tokens for each request in the batch.
+    # Currently, we require that all requests have the same number of query
+    # tokens during the decoding phase. When speculavie decoding is enabled,
+    # decode_query_len might be greater than 1. In all other cases, it is 1.
+    decode_query_len: Optional[int] = None
+
     _cached_prefill_metadata: Optional[
         "BlocksparseFlashAttentionMetadata"] = None
     _cached_decode_metadata: Optional[
diff --git a/vllm/attention/backends/flash_attn.py b/vllm/attention/backends/flash_attn.py
index 43ca6c9ff160..e27702336719 100644
--- a/vllm/attention/backends/flash_attn.py
+++ b/vllm/attention/backends/flash_attn.py
@@ -245,8 +245,15 @@ class FlashAttentionMetadata(AttentionMetadata):
     # |-------------------- seq_len ---------------------|
     #                                   |-- query_len ---|
 
-    # Maximum query length in the batch. None for decoding.
+    # Maximum query length in the batch.
     max_query_len: Optional[int]
+
+    # Number of query tokens for each request in the batch.
+    # Currently, we require that all requests have the same number of query
+    # tokens during the decoding phase. When speculavie decoding is enabled,
+    # decode_query_len might be greater than 1. In all other cases, it is 1.
+    decode_query_len: Optional[int]
+
     # Maximum sequence length among prefill batch. 0 if there are decoding
     # requests only.
     max_prefill_seq_len: int
@@ -303,6 +310,7 @@ def prefill_metadata(self) -> Optional["FlashAttentionMetadata"]:
             slot_mapping=self.slot_mapping[:self.num_prefill_tokens],
             seq_lens=self.seq_lens[:self.num_prefills],
             seq_lens_tensor=self.seq_lens_tensor[:self.num_prefills],
+            decode_query_len=0,
             max_query_len=self.max_query_len,
             max_prefill_seq_len=self.max_prefill_seq_len,
             max_decode_seq_len=0,
@@ -331,7 +339,8 @@ def decode_metadata(self) -> Optional["FlashAttentionMetadata"]:
             slot_mapping=self.slot_mapping[self.num_prefill_tokens:],
             seq_lens=None,
             seq_lens_tensor=self.seq_lens_tensor[self.num_prefills:],
-            max_query_len=None,
+            decode_query_len=self.decode_query_len,
+            max_query_len=self.max_query_len,
             max_prefill_seq_len=0,
             max_decode_seq_len=self.max_decode_seq_len,
             query_start_loc=None,
@@ -461,9 +470,6 @@ def _add_seq_group(
                 self.num_prefill_tokens += token_len
                 self.prefill_seq_lens.append(seq_len)
             else:
-                assert query_len == 1, (
-                    "seq_len: {}, context_len: {}, query_len: {}".format(
-                        seq_len, context_len, query_len))
                 self.num_decode_tokens += query_len
                 self.curr_seq_lens.append(curr_seq_len)
 
@@ -518,6 +524,11 @@ def build(self, seq_lens: List[int], query_lens: List[int],
         use_captured_graph = cuda_graph_pad_size != -1
 
         max_query_len = max(query_lens)
+        decode_query_lens = query_lens[self.num_prefills:]
+        if len(decode_query_lens) > 0:
+            decode_query_len = max(decode_query_lens)
+        else:
+            decode_query_len = 1
         max_prefill_seq_len = max(self.prefill_seq_lens, default=0)
         max_decode_seq_len = max(self.curr_seq_lens, default=0)
         num_decode_tokens = self.num_decode_tokens
@@ -586,6 +597,7 @@ def build(self, seq_lens: List[int], query_lens: List[int],
             seq_lens=seq_lens,
             seq_lens_tensor=seq_lens_tensor,
             max_query_len=max_query_len,
+            decode_query_len=decode_query_len,
             max_prefill_seq_len=max_prefill_seq_len,
             max_decode_seq_len=max_decode_seq_len,
             query_start_loc=query_start_loc,
@@ -786,8 +798,12 @@ def forward(
 
         if decode_meta := attn_metadata.decode_metadata:
             # Decoding run.
+            _, num_head, head_dim = decode_query.shape
+            decode_query = decode_query.reshape(-1,
+                                                decode_meta.decode_query_len,
+                                                num_head, head_dim)
             decode_output = torch.ops.vllm.flash_attn_with_kvcache(
-                decode_query.unsqueeze(1),
+                decode_query,
                 key_cache,
                 value_cache,
                 block_table=decode_meta.block_tables,
@@ -796,7 +812,7 @@ def forward(
                 causal=True,
                 alibi_slopes=self.alibi_slopes,
                 softcap=self.logits_soft_cap,
-            ).squeeze(1)
+            )
 
         if prefill_output is None:
             assert decode_output is not None
@@ -804,5 +820,11 @@ def forward(
         if decode_output is None:
             assert prefill_output is not None
             return prefill_output.view(num_prefill_tokens, hidden_size)
+
+        # Chunked prefill does not work with speculative decoding.
+        # Therefore, the query length for decode should be 1 in chunked prefill.
+        assert decode_meta is not None
+        assert decode_meta.decode_query_len == 1
+        decode_output = decode_output.squeeze(1)
         output = torch.cat([prefill_output, decode_output], dim=0)
         return output.view(num_tokens, hidden_size)
diff --git a/vllm/attention/backends/flashinfer.py b/vllm/attention/backends/flashinfer.py
index a64bf34596f9..96d37b99f201 100644
--- a/vllm/attention/backends/flashinfer.py
+++ b/vllm/attention/backends/flashinfer.py
@@ -595,7 +595,6 @@ def build(self, seq_lens: List[int], query_lens: List[int],
         device = self.runner.device
         use_captured_graph = cuda_graph_pad_size != -1
 
-        max_query_len = max(query_lens)
         max_prefill_seq_len = max(self.prefill_seq_lens, default=0)
         num_decode_tokens = self.num_decode_tokens
 
@@ -634,7 +633,6 @@ def build(self, seq_lens: List[int], query_lens: List[int],
                 dtype=torch.int,
                 device=device,
             )
-        assert max_query_len > 0, ("query_lens: {}".format(query_lens))
 
         assert device is not None
         seq_lens_tensor = async_tensor_h2d(seq_lens, torch.int, device,
diff --git a/vllm/attention/backends/rocm_flash_attn.py b/vllm/attention/backends/rocm_flash_attn.py
index 5ee3c3b69cf3..fb5cd11ec033 100644
--- a/vllm/attention/backends/rocm_flash_attn.py
+++ b/vllm/attention/backends/rocm_flash_attn.py
@@ -116,9 +116,17 @@ class ROCmFlashAttentionMetadata(AttentionMetadata, PagedAttentionMetadata):
     # Cuda-graph is currently enabled for decoding only.
     # TODO(woosuk): Move `use_cuda_graph` out since it's unrelated to attention.
     use_cuda_graph: bool
+
     # (batch_size,) A tensor of context lengths (tokens that are computed
     # so far).
     context_lens_tensor: Optional[torch.Tensor]
+
+    # Number of query tokens for each request in the batch.
+    # Currently, we require that all requests have the same number of query
+    # tokens during the decoding phase. When speculavie decoding is enabled,
+    # decode_query_len might be greater than 1. In all other cases, it is 1.
+    decode_query_len: Optional[int] = None
+
     _cached_prefill_metadata: Optional["ROCmFlashAttentionMetadata"] = None
     _cached_decode_metadata: Optional["ROCmFlashAttentionMetadata"] = None
 
diff --git a/vllm/attention/backends/utils.py b/vllm/attention/backends/utils.py
index 49fbb25f4547..2b8c373178ab 100644
--- a/vllm/attention/backends/utils.py
+++ b/vllm/attention/backends/utils.py
@@ -312,7 +312,8 @@ def graph_capture_get_metadata_for_batch(
             slot_mapping=self._graph_slot_mapping[:batch_size],
             seq_lens=None,
             seq_lens_tensor=self._graph_seq_lens[:batch_size],
-            max_query_len=None,
+            max_query_len=1,
+            decode_query_len=1,
             max_prefill_seq_len=0,
             max_decode_seq_len=self.runner.max_seq_len_to_capture,
             query_start_loc=None,
diff --git a/vllm/attention/backends/xformers.py b/vllm/attention/backends/xformers.py
index 143fa6ee7dea..a3f9ff64f8b8 100644
--- a/vllm/attention/backends/xformers.py
+++ b/vllm/attention/backends/xformers.py
@@ -118,6 +118,12 @@ class XFormersMetadata(AttentionMetadata, PagedAttentionMetadata):
     # Maximum query length in the batch. None for decoding.
     max_query_len: Optional[int] = None
 
+    # Number of query tokens for each request in the batch.
+    # Currently, we require that all requests have the same number of query
+    # tokens during the decoding phase. When speculavie decoding is enabled,
+    # decode_query_len might be greater than 1. In all other cases, it is 1.
+    decode_query_len: Optional[int] = None
+
     # (batch_size + 1,). The cumulative subquery lengths of the sequences in
     # the batch, used to index into subquery. E.g., if the subquery length
     # is [4, 6], it is [0, 4, 10].
diff --git a/vllm/config.py b/vllm/config.py
index 3139c5a08bfb..1310c07ade48 100644
--- a/vllm/config.py
+++ b/vllm/config.py
@@ -1116,6 +1116,7 @@ def maybe_create_spec_config(
         speculative_model_quantization: Optional[str],
         speculative_draft_tensor_parallel_size: Optional[int],
         num_speculative_tokens: Optional[int],
+        speculative_disable_mqa_scorer: Optional[bool],
         speculative_max_model_len: Optional[int],
         enable_chunked_prefill: bool,
         use_v2_block_manager: bool,
@@ -1150,6 +1151,9 @@ def maybe_create_spec_config(
             num_speculative_tokens (Optional[int]): The number of speculative
                 tokens, if provided. Will default to the number in the draft
                 model config if present, otherwise is required.
+            speculative_disable_mqa_scorer (Optional[bool]): Disable the MQA
+                scorer for the speculative model and fall back to batch
+                expansion for scoring.
             speculative_max_model_len (Optional[int]): The maximum model len of
                 the speculative model. Used when testing the ability to skip
                 speculation for some sequences.
@@ -1304,6 +1308,7 @@ def maybe_create_spec_config(
             draft_model_config,
             draft_parallel_config,
             num_speculative_tokens,
+            speculative_disable_mqa_scorer,
             speculative_disable_by_batch_size,
             ngram_prompt_lookup_max,
             ngram_prompt_lookup_min,
@@ -1400,6 +1405,7 @@ def __init__(
         draft_model_config: ModelConfig,
         draft_parallel_config: ParallelConfig,
         num_speculative_tokens: int,
+        speculative_disable_mqa_scorer: Optional[bool],
         speculative_disable_by_batch_size: Optional[int],
         ngram_prompt_lookup_max: Optional[int],
         ngram_prompt_lookup_min: Optional[int],
@@ -1446,6 +1452,7 @@ def __init__(
         self.draft_model_config = draft_model_config
         self.draft_parallel_config = draft_parallel_config
         self.num_speculative_tokens = num_speculative_tokens
+        self.speculative_disable_mqa_scorer = speculative_disable_mqa_scorer
         self.speculative_disable_by_batch_size = \
             speculative_disable_by_batch_size
         self.ngram_prompt_lookup_max = ngram_prompt_lookup_max or 0
diff --git a/vllm/engine/arg_utils.py b/vllm/engine/arg_utils.py
index 208766a18e99..64fa7360b95b 100644
--- a/vllm/engine/arg_utils.py
+++ b/vllm/engine/arg_utils.py
@@ -162,6 +162,7 @@ class EngineArgs:
     speculative_model_quantization: Optional[str] = None
     speculative_draft_tensor_parallel_size: Optional[int] = None
     num_speculative_tokens: Optional[int] = None
+    speculative_disable_mqa_scorer: Optional[bool] = False
     speculative_max_model_len: Optional[int] = None
     speculative_disable_by_batch_size: Optional[int] = None
     ngram_prompt_lookup_max: Optional[int] = None
@@ -640,6 +641,12 @@ def add_cli_args(parser: FlexibleArgumentParser) -> FlexibleArgumentParser:
             default=EngineArgs.num_speculative_tokens,
             help='The number of speculative tokens to sample from '
             'the draft model in speculative decoding.')
+        parser.add_argument(
+            '--speculative-disable-mqa-scorer',
+            action='store_true',
+            help=
+            'If set to True, the MQA scorer will be disabled in speculative '
+            ' and fall back to batch expansion')
         parser.add_argument(
             '--speculative-draft-tensor-parallel-size',
             '-spec-draft-tp',
@@ -970,6 +977,7 @@ def create_engine_config(self) -> EngineConfig:
             speculative_draft_tensor_parallel_size = \
                 self.speculative_draft_tensor_parallel_size,
             num_speculative_tokens=self.num_speculative_tokens,
+            speculative_disable_mqa_scorer=self.speculative_disable_mqa_scorer,
             speculative_disable_by_batch_size=self.
             speculative_disable_by_batch_size,
             speculative_max_model_len=self.speculative_max_model_len,
diff --git a/vllm/engine/llm_engine.py b/vllm/engine/llm_engine.py
index 3550759f85dd..d6258c6413d8 100644
--- a/vllm/engine/llm_engine.py
+++ b/vllm/engine/llm_engine.py
@@ -1110,6 +1110,8 @@ def update_prefill_num_computed_tokens(
                 update_prefill_num_computed_tokens(seq_group, seq_group_meta,
                                                    len(output),
                                                    is_first_step_output)
+            elif not is_async:
+                seq_group.update_num_computed_tokens(1)
 
             if outputs:
                 for o in outputs:
@@ -1133,8 +1135,16 @@ def update_prefill_num_computed_tokens(
             else:
                 self.output_processor.process_prompt_logprob(seq_group, output)
                 if seq_group_meta.do_sample:
-                    self.output_processor.process_outputs(
+                    output_token_num = self.output_processor.process_outputs(
                         seq_group, output, is_async)
+                    if self.speculative_config:
+                        # We -1 here because we always
+                        # (w/o speculative decoding) add the number of
+                        # computed tokens by one in the decoding phase.
+                        # Therefore, we remove that one token that
+                        # is already added.
+                        seq_group.update_num_computed_tokens(output_token_num -
+                                                             1)
 
             if seq_group.is_finished():
                 finished_now.append(i)
@@ -1251,11 +1261,12 @@ def _advance_to_next_step(
                     # decodes after the very first step. Therefore,
                     # we skip the update to the num_computed_tokens
                     # here.
-                    pass
+                    seq_group.update_num_computed_tokens(1)
                 else:
                     seq_group.update_num_computed_tokens(
                         seq_group_metadata.token_chunk_size)
-
+            else:
+                seq_group.update_num_computed_tokens(1)
             if seq_group_metadata.do_sample:
                 assert len(sequence_group_outputs.samples) == 1, (
                     "Async output processor expects a single sample"
@@ -1266,7 +1277,6 @@ def _advance_to_next_step(
                 assert len(seq_group.seqs) == 1
                 seq = seq_group.seqs[0]
                 seq.append_token_id(sample.output_token, sample.logprobs)
-                seq_group.update_num_computed_tokens(1)
 
     def step(self) -> List[Union[RequestOutput, EmbeddingRequestOutput]]:
         """Performs one decoding iteration and returns newly generated results.
diff --git a/vllm/engine/output_processor/interfaces.py b/vllm/engine/output_processor/interfaces.py
index 50adaf4e5918..554880a3cc43 100644
--- a/vllm/engine/output_processor/interfaces.py
+++ b/vllm/engine/output_processor/interfaces.py
@@ -1,5 +1,5 @@
 from abc import ABC, abstractmethod
-from typing import Callable, List
+from typing import Callable, List, Optional
 
 from vllm.config import SchedulerConfig
 from vllm.core.scheduler import Scheduler
@@ -58,10 +58,14 @@ def create_output_processor(
     @abstractmethod
     def process_outputs(self, sequence_group: SequenceGroup,
                         outputs: List[SequenceGroupOutput],
-                        is_async: bool) -> None:
+                        is_async: bool) -> Optional[int]:
         """Process new token ids for the sequence group. Handles logic such as
         detokenization, stop checking, and freeing/forking sequences in the
         scheduler.
+        
+        Return the number of new tokens generated in the sequence group.
+        The returned value is optional because it is only used for 
+        speculative decoding mqa scorer.
         """
         pass
 
diff --git a/vllm/engine/output_processor/multi_step.py b/vllm/engine/output_processor/multi_step.py
index 6dac3619580b..f35b1ba9c2bd 100644
--- a/vllm/engine/output_processor/multi_step.py
+++ b/vllm/engine/output_processor/multi_step.py
@@ -1,5 +1,5 @@
 import functools
-from typing import Callable, List
+from typing import Callable, List, Optional
 
 from vllm.core.scheduler import Scheduler
 from vllm.engine.output_processor.interfaces import (
@@ -69,7 +69,7 @@ def _log_prompt_logprob_unsupported_warning_once():
     def process_outputs(self,
                         sequence_group: SequenceGroup,
                         outputs: List[SequenceGroupOutput],
-                        is_async: bool = False) -> None:
+                        is_async: bool = False) -> Optional[int]:
         """Append new tokens in the outputs to sequences in the sequence group.
 
         This only supports sequence groups of size 1. It supports greater than
@@ -84,6 +84,10 @@ def process_outputs(self,
             tokens from the previous step. If this is true, then
             no tokens need to be appended since it is already done
             externally (before the next schedule() call)
+            
+        Returns:
+            The number of tokens appended to the sequence. This is optional
+            because only speculative decode uses this return value.
         """
         # Sequences can be in RUNNING or FINISHED_ABORTED state
         # once scheduled, as a sequence is moved to FINSIHED_ABORTED
@@ -106,6 +110,7 @@ def process_outputs(self,
             # was already appended, so we only need to do the rest of the
             # postprocessor: Detokenization + stopping logic
             self._process_decode_and_stop(seq, sequence_group.sampling_params)
+            return None
         else:
             # Standard multi-step case
 
@@ -121,8 +126,8 @@ def process_outputs(self,
             ]
             assert valid_samples
 
-            self._process_seq_outputs(seq, valid_samples,
-                                      sequence_group.sampling_params)
+            return self._process_seq_outputs(seq, valid_samples,
+                                             sequence_group.sampling_params)
 
     def _process_decode_and_stop(self, seq: Sequence,
                                  sampling_params: SamplingParams) -> None:
@@ -140,7 +145,7 @@ def _process_decode_and_stop(self, seq: Sequence,
 
     def _process_seq_outputs(self, seq: Sequence,
                              valid_samples: List[SequenceOutput],
-                             sampling_params: SamplingParams) -> None:
+                             sampling_params: SamplingParams) -> int:
         output_token_ids = [sample.output_token for sample in valid_samples]
         output_logprobs = [sample.logprobs for sample in valid_samples]
 
@@ -148,7 +153,6 @@ def _process_seq_outputs(self, seq: Sequence,
         remaining_tokens = sampling_params.max_tokens - (seq.get_output_len() +
                                                          len(output_token_ids))
         if remaining_tokens < 0:
-            valid_samples = valid_samples[:remaining_tokens]
             output_token_ids = output_token_ids[:remaining_tokens]
 
         # Truncate any tokens after EOS. This is required as spec decode
@@ -162,7 +166,6 @@ def _process_seq_outputs(self, seq: Sequence,
             for i in range(len(output_token_ids)):
                 if output_token_ids[i] == eos_token_id:
                     output_token_ids = output_token_ids[:i + 1]
-                    valid_samples = valid_samples[:i + 1]
                     break
 
         # Incrementally append tokens to the sequence, as if we had only one new
@@ -173,9 +176,9 @@ def _process_seq_outputs(self, seq: Sequence,
                 token_id=output_token_id,
                 logprobs=output_logprob,
             )
-            seq.data.update_num_computed_tokens(1)
 
             self._process_decode_and_stop(seq, sampling_params)
 
             if seq.is_finished():
                 break
+        return len(output_token_ids)
diff --git a/vllm/model_executor/layers/sampler.py b/vllm/model_executor/layers/sampler.py
index 583bb02dcb5b..cfa857b8f960 100644
--- a/vllm/model_executor/layers/sampler.py
+++ b/vllm/model_executor/layers/sampler.py
@@ -912,7 +912,7 @@ def get_logprobs(
     sampling_metadata: SamplingMetadata,
     sample_results: SampleResultType,
 ) -> Tuple[List[Optional[PromptLogprobs]], List[SampleLogprobs]]:
-    """Return sample lobprobs and prompt logprobs.
+    """Return sample logprobs and prompt logprobs.
 
     The logic consists of 3 parts.
     - Select indices to compute logprob from, ranks of token ids, and
diff --git a/vllm/model_executor/sampling_metadata.py b/vllm/model_executor/sampling_metadata.py
index 97d36d31f2b1..ee02368bec8a 100644
--- a/vllm/model_executor/sampling_metadata.py
+++ b/vllm/model_executor/sampling_metadata.py
@@ -146,7 +146,7 @@ def __init__(
     def prepare(
         seq_group_metadata_list: List[SequenceGroupMetadata],
         seq_lens: List[int],
-        query_lens: Optional[List[int]],
+        query_lens: List[int],
         device: str,
         pin_memory: bool,
         generators: Optional[Dict[str, torch.Generator]] = None,
@@ -194,7 +194,7 @@ def __repr__(self) -> str:
 def _prepare_seq_groups(
     seq_group_metadata_list: List[SequenceGroupMetadata],
     seq_lens: List[int],
-    query_lens: Optional[List[int]],
+    query_lens: List[int],
     device: str,
     generators: Optional[Dict[str, torch.Generator]] = None,
     cache: Optional[SamplingMetadataCache] = None,
@@ -284,7 +284,8 @@ def _prepare_seq_groups(
         else:
             # Decode
             prompt_logprob_len = 0
-            sample_len = len(seq_ids) if do_sample else 0
+            query_len = query_lens[i] if query_lens is not None else 1
+            sample_len = len(seq_ids) * query_len if do_sample else 0
 
             if sampling_params.seed is not None and generators is not None:
                 generator = generators.get(seq_group_metadata.request_id)
@@ -440,14 +441,14 @@ def from_sampling_metadata(
 
             if seq_group.do_sample:
                 sample_lens = len(seq_group.sample_indices)
-                assert sample_lens == len(seq_ids)
-                temperatures += [temperature] * len(seq_ids)
-                top_ps += [top_p] * len(seq_ids)
-                top_ks += [top_k] * len(seq_ids)
-                min_ps += [min_p] * len(seq_ids)
-                presence_penalties += [p] * len(seq_ids)
-                frequency_penalties += [f] * len(seq_ids)
-                repetition_penalties += [r] * len(seq_ids)
+                assert sample_lens >= len(seq_ids)
+                temperatures += [temperature] * sample_lens
+                top_ps += [top_p] * sample_lens
+                top_ks += [top_k] * sample_lens
+                min_ps += [min_p] * sample_lens
+                presence_penalties += [p] * sample_lens
+                frequency_penalties += [f] * sample_lens
+                repetition_penalties += [r] * sample_lens
 
         if do_penalties:
             for seq_group in sampling_metadata.seq_groups:
diff --git a/vllm/spec_decode/batch_expansion.py b/vllm/spec_decode/batch_expansion.py
index 9eb8bbfc5407..59e71cc8deb4 100644
--- a/vllm/spec_decode/batch_expansion.py
+++ b/vllm/spec_decode/batch_expansion.py
@@ -12,7 +12,6 @@
 from vllm.spec_decode.interfaces import (SpeculativeProposals,
                                          SpeculativeScorer, SpeculativeScores)
 from vllm.spec_decode.util import nvtx_range, split_batch_by_proposal_len
-from vllm.worker.worker_base import WorkerBase
 
 SeqId = int
 TargetSeqId = int
@@ -36,12 +35,6 @@ class BatchExpansionTop1Scorer(SpeculativeScorer):
     of topk/tree.
     """
 
-    def __init__(self, scorer_worker: WorkerBase, device: str,
-                 vocab_size: int):
-        self._scorer_worker = scorer_worker
-        self._device = device
-        self._vocab_size = vocab_size
-
     @nvtx_range("BatchExpansionTop1Scorer.score_proposals")
     def score_proposals(
         self,
diff --git a/vllm/spec_decode/draft_model_runner.py b/vllm/spec_decode/draft_model_runner.py
index cf64af72a14a..71cba5dd25f6 100644
--- a/vllm/spec_decode/draft_model_runner.py
+++ b/vllm/spec_decode/draft_model_runner.py
@@ -94,8 +94,6 @@ def _update_sampling_metadata(self, sampling_metadata, num_seqs,
             assert seq_group.is_prompt is False  # No prompt
             assert seq_group.prompt_logprob_indices == []  # No prompt
             assert seq_group.sample_indices == [i]  # Simple
-            assert seq_group.seq_len is None  # Decode
-            assert seq_group.query_len is None  # Decode
 
     def _gpu_advance_step(
             self, model_input: ModelInputForGPUWithSamplingMetadata,
diff --git a/vllm/spec_decode/interfaces.py b/vllm/spec_decode/interfaces.py
index 11ab09f10c1f..029f56460f5c 100644
--- a/vllm/spec_decode/interfaces.py
+++ b/vllm/spec_decode/interfaces.py
@@ -5,6 +5,7 @@
 import torch
 
 from vllm.sequence import ExecuteModelRequest
+from vllm.worker.worker_base import WorkerBase
 
 
 @dataclass
@@ -74,6 +75,12 @@ def get_spec_proposals(
 
 class SpeculativeScorer(ABC):
 
+    def __init__(self, scorer_worker: WorkerBase, device: str,
+                 vocab_size: int):
+        self._scorer_worker = scorer_worker
+        self._device = device
+        self._vocab_size = vocab_size
+
     @abstractmethod
     def score_proposals(
         self,
diff --git a/vllm/spec_decode/mqa_scorer.py b/vllm/spec_decode/mqa_scorer.py
new file mode 100644
index 000000000000..59f2a4191a8b
--- /dev/null
+++ b/vllm/spec_decode/mqa_scorer.py
@@ -0,0 +1,80 @@
+from vllm.sequence import (ExecuteModelRequest, SequenceData,
+                           SequenceGroupMetadata, get_all_seq_ids)
+from vllm.spec_decode.interfaces import (SpeculativeProposals,
+                                         SpeculativeScorer, SpeculativeScores)
+
+SeqId = int
+TargetSeqId = int
+
+
+class MQAScorer(SpeculativeScorer):
+
+    def score_proposals(
+        self,
+        execute_model_req: ExecuteModelRequest,
+        proposals: SpeculativeProposals,
+    ) -> SpeculativeScores:
+        target_seq_group_metadata_list = []
+        target_seq_id_start = max(
+            get_all_seq_ids(execute_model_req.seq_group_metadata_list)) + 1
+        all_proposal_tokens = proposals.proposal_token_ids.tolist()
+        for i, seq_group_metadata in enumerate(
+                execute_model_req.seq_group_metadata_list):
+            seq_data_dict = seq_group_metadata.seq_data
+            assert len(seq_data_dict) == 1
+            seq_id = next(iter(seq_data_dict.keys()))
+
+            seq_data: SequenceData = seq_data_dict[seq_id]
+            prompt_token_ids = seq_data.get_prompt_token_ids()
+            output_token_ids = seq_data.get_output_token_ids()
+            proposal_token_ids = all_proposal_tokens[i]
+            new_output_token_ids = [*output_token_ids, *proposal_token_ids]
+
+            target_seq_id = target_seq_id_start + i
+            new_seq_data = SequenceData.from_seqs(
+                prompt_token_ids=prompt_token_ids,
+                output_token_ids=new_output_token_ids,
+            )
+            new_seq_data.update_num_computed_tokens(
+                len(prompt_token_ids) + len(output_token_ids) - 1)
+
+            # Ensure that the new sequence has at least one token
+            # because we only use mqa scorer in the decoding stage.
+            assert len(output_token_ids) >= 1
+            new_seq_data_dict = {target_seq_id: new_seq_data}
+
+            new_seq_group_metadata = SequenceGroupMetadata(
+                request_id=seq_group_metadata.request_id,
+                is_prompt=seq_group_metadata.is_prompt,
+                seq_data=new_seq_data_dict,
+                sampling_params=seq_group_metadata.sampling_params,
+                block_tables={
+                    target_seq_id: seq_group_metadata.block_tables[seq_id],
+                },
+                lora_request=None,
+                token_chunk_size=1,
+            )
+            target_seq_group_metadata_list.append(new_seq_group_metadata)
+
+        target_sampler_output = self._scorer_worker.execute_model(
+            execute_model_req=execute_model_req.clone(
+                seq_group_metadata_list=target_seq_group_metadata_list))
+
+        target_sampler_output = target_sampler_output[0]
+
+        bs, k = proposals.proposal_token_ids.shape
+        all_tokens = target_sampler_output.sampled_token_ids.reshape(bs, k + 1)
+
+        all_probs = target_sampler_output.sampled_token_probs.reshape(
+            bs, k + 1, self._vocab_size)
+        all_logprobs = target_sampler_output.logprobs.reshape(
+            bs, k + 1, self._vocab_size)
+
+        hidden_states = None
+        if target_sampler_output.hidden_states is not None:
+            hidden_states = target_sampler_output.hidden_states.reshape(
+                bs, (k + 1), -1)
+        return SpeculativeScores(probs=all_probs,
+                                 token_ids=all_tokens,
+                                 logprobs=all_logprobs,
+                                 hidden_states=hidden_states)
diff --git a/vllm/spec_decode/spec_decode_worker.py b/vllm/spec_decode/spec_decode_worker.py
index dbf880a8f475..a67715290a51 100644
--- a/vllm/spec_decode/spec_decode_worker.py
+++ b/vllm/spec_decode/spec_decode_worker.py
@@ -1,6 +1,6 @@
 from collections import defaultdict
 from functools import cached_property
-from typing import Any, Dict, List, Optional, Set, Tuple
+from typing import Any, Dict, List, Optional, Set, Tuple, Type
 
 import torch
 
@@ -24,6 +24,7 @@
 from vllm.spec_decode.medusa_worker import MedusaWorker
 from vllm.spec_decode.metrics import AsyncMetricsCollector
 from vllm.spec_decode.mlp_speculator_worker import MLPSpeculatorWorker
+from vllm.spec_decode.mqa_scorer import MQAScorer
 from vllm.spec_decode.multi_step_worker import MultiStepWorker
 from vllm.spec_decode.ngram_worker import NGramWorker
 from vllm.spec_decode.proposer_worker_base import ProposerWorkerBase
@@ -70,6 +71,7 @@ def create_spec_worker(*args, **kwargs) -> "SpecDecodeWorker":
     spec_decode_worker = SpecDecodeWorker.create_worker(
         scorer_worker=target_worker,
         draft_worker_kwargs=draft_worker_kwargs,
+        disable_mqa_scorer=speculative_config.speculative_disable_mqa_scorer,
         disable_by_batch_size=speculative_config.
         speculative_disable_by_batch_size,
         draft_token_acceptance_method=speculative_config.
@@ -116,6 +118,7 @@ def create_worker(
         cls,
         scorer_worker: Worker,
         draft_worker_kwargs: Dict[str, Any],
+        disable_mqa_scorer: bool,
         disable_by_batch_size: Optional[int],
         draft_token_acceptance_method: str,
         typical_acceptance_sampler_posterior_threshold: float,
@@ -173,12 +176,43 @@ def create_worker(
                     typical_acceptance_sampler_posterior_threshold,
                 posterior_alpha=typical_acceptance_sampler_posterior_alpha,
             )
-        logger.info("Configuring SpecDecodeWorker with sampler=%s",
-                    type(spec_decode_sampler))
+        logger.info(
+            "[Speculative Decoding] Configuring"
+            " SpecDecodeWorker with sampler=%s", type(spec_decode_sampler))
+
+        if not disable_mqa_scorer:
+            if scorer_worker.model_runner.attn_backend.get_name(
+            ) != "flash-attn":
+                disable_mqa_scorer = True
+                logger.info(
+                    "[Speculative Decoding] Disabling MQA scorer as the "
+                    "MQA is only available with flash attn backend.")
+
+            if ngram_prompt_lookup_max > 0:
+                disable_mqa_scorer = True
+                logger.info(
+                    "[Speculative Decoding] Disabling MQA scorer as the "
+                    "NGramWorker does not support MQA scorer.")
+
+            if "model_config" in draft_worker_kwargs and \
+                draft_worker_kwargs["model_config"].max_model_len < \
+                    scorer_worker.model_config.max_model_len:
+                disable_mqa_scorer = True
+                logger.info(
+                    "[Speculative Decoding] Disabling MQA scorer as the "
+                    "draft model max_model_len is smaller than the target "
+                    "model max_model_len.")
+
+            if not scorer_worker.model_runner.model_config.enforce_eager:
+                disable_mqa_scorer = True
+                logger.info(
+                    "[Speculative Decoding] Disabling MQA scorer as the "
+                    "target model is not running in eager mode.")
 
         return SpecDecodeWorker(
             proposer_worker,
             scorer_worker,
+            disable_mqa_scorer=disable_mqa_scorer,
             disable_logprobs=disable_logprobs,
             disable_log_stats=disable_log_stats,
             disable_by_batch_size=disable_by_batch_size,
@@ -190,6 +224,7 @@ def __init__(
         proposer_worker: ProposerWorkerBase,
         scorer_worker: WorkerBase,
         spec_decode_sampler: SpecDecodeBaseSampler,
+        disable_mqa_scorer: bool = False,
         disable_logprobs: bool = False,
         disable_log_stats: bool = False,
         metrics_collector: Optional[AsyncMetricsCollector] = None,
@@ -211,6 +246,8 @@ def __init__(
                 types of sampler namely RejectionSampler and
                 TypicalAcceptanceSampler. 'spec_decode_sampler' is either an
                 instance of RejectionSampler or TypicalAcceptanceSampler.
+            disable_mqa_scorer: If set to True, disable the MQA scorer and use
+                the BatchExpansionTop1Scorer instead.
             disable_logprobs: If set to True, token log probabilities will
                 not be output in both the draft worker and the target worker.
                 If set to False, log probabilities will be output by both.
@@ -248,6 +285,7 @@ def __init__(
         self.token_id_dtype = self.spec_decode_sampler.token_id_dtype
         # Lazy initialization.
         self.scorer: SpeculativeScorer
+        self.disable_mqa_scorer = disable_mqa_scorer
 
         # Hidden states from target model to pass to proposer
         # in the subsequent step.
@@ -270,10 +308,19 @@ def init_device(self) -> None:
         self._metrics.init_gpu_tensors(self.rank)
         self.spec_decode_sampler.init_gpu_tensors(self.rank)
 
-        self.scorer = BatchExpansionTop1Scorer(
-            scorer_worker=self.scorer_worker,
-            device=self.device,
-            vocab_size=self._vocab_size)
+        scorer_cls: Type[SpeculativeScorer]
+        if self.disable_mqa_scorer:
+            scorer_cls = BatchExpansionTop1Scorer
+            logger.info("[Speculative Decoding] Use batch "
+                        "expansion for scoring proposals.")
+        else:
+            scorer_cls = MQAScorer
+            logger.info(
+                "[Speculative Decoding] Use MQA scorer for scoring proposals.")
+
+        self.scorer = scorer_cls(scorer_worker=self.scorer_worker,
+                                 device=self.device,
+                                 vocab_size=self._vocab_size)
 
         self._configure_model_sampler_for_spec_decode()
 
diff --git a/vllm/worker/model_runner.py b/vllm/worker/model_runner.py
index 76c04ce66fc2..bd92abdb945d 100644
--- a/vllm/worker/model_runner.py
+++ b/vllm/worker/model_runner.py
@@ -468,43 +468,26 @@ def _compute_lens(self, inter_data: InterDataForSeqGroup, seq_idx: int,
 
         # Compute context length (the number of tokens that are
         # already computed) and sequence length (total number of tokens).
+
         seq_len = seq_data.get_len()
         if inter_data.is_prompt:
             context_len = seq_data.get_num_computed_tokens()
-        else:
-            # get_num_computed_tokens is incorrect for spec decoding.
-            # So, we should have a special logic here.
-            # TODO(sang): Fix it.
+            seq_len = min(seq_len, context_len + token_chunk_size)
+        elif self.runner.scheduler_config.is_multi_step or \
+            self.runner.model_config.is_encoder_decoder_model:
             context_len = seq_len - 1
-        seq_len = min(seq_len, context_len + token_chunk_size)
+        else:
+            context_len = seq_data.get_num_computed_tokens()
 
         # Compute tokens.
-        if inter_data.is_prompt:
-            tokens = seq_data.get_token_ids()
-            if context_len != 0 or seq_len < len(tokens):
-                tokens = tokens[context_len:seq_len]
-        else:
-            # Optimization. get_token_ids requires the entire copy of
-            # tokens.
-            tokens = seq_data.get_last_token_id()
+        tokens = seq_data.get_token_ids()[context_len:seq_len]
 
         inter_data.seq_lens[seq_idx] = seq_len
         inter_data.orig_seq_lens[seq_idx] = seq_len
         inter_data.context_lens[seq_idx] = context_len
-
-        if isinstance(tokens, list):
-            inter_data.input_tokens[seq_idx].extend(tokens)
-        else:
-            inter_data.input_tokens[seq_idx].append(tokens)
-
-        if (seq_len - context_len) == 1:
-            inter_data.input_positions[seq_idx].append(seq_len - 1)
-        else:
-            inter_data.input_positions[seq_idx].extend(
-                range(context_len, seq_len))
-
-        inter_data.query_lens[
-            seq_idx] = seq_len - context_len if inter_data.is_prompt else 1
+        inter_data.input_tokens[seq_idx].extend(tokens)
+        inter_data.input_positions[seq_idx].extend(range(context_len, seq_len))
+        inter_data.query_lens[seq_idx] = seq_len - context_len
 
         if seq_data.mrope_position_delta is not None:
             if inter_data.mrope_input_positions is None: