diff --git a/crates/l2/sequencer/l1_committer.rs b/crates/l2/sequencer/l1_committer.rs
index 6adb69105b1..b11b2fd85c4 100644
--- a/crates/l2/sequencer/l1_committer.rs
+++ b/crates/l2/sequencer/l1_committer.rs
@@ -4,7 +4,8 @@ use crate::{
     sequencer::{
         errors::CommitterError,
         utils::{
-            self, fetch_blocks_with_respective_fee_configs, get_git_commit_hash, system_now_ms,
+            self, batch_checkpoint_name, fetch_blocks_with_respective_fee_configs,
+            get_git_commit_hash, system_now_ms,
         },
     },
 };
@@ -1313,7 +1314,3 @@ pub async fn regenerate_head_state(
 
     Ok(())
 }
-
-fn batch_checkpoint_name(batch_number: u64) -> String {
-    format!("checkpoint_batch_{batch_number}")
-}
diff --git a/crates/l2/sequencer/l1_proof_sender.rs b/crates/l2/sequencer/l1_proof_sender.rs
index 7cc89978b20..d68a220b932 100644
--- a/crates/l2/sequencer/l1_proof_sender.rs
+++ b/crates/l2/sequencer/l1_proof_sender.rs
@@ -1,4 +1,8 @@
-use std::collections::{BTreeMap, HashMap};
+use std::{
+    collections::{BTreeMap, HashMap},
+    fs::remove_dir_all,
+    path::PathBuf,
+};
 
 use ethrex_common::{Address, U256};
 use ethrex_l2_common::{
@@ -30,7 +34,7 @@ use super::{
 use crate::{
     CommitterConfig, EthConfig, ProofCoordinatorConfig, SequencerConfig,
     based::sequencer_state::{SequencerState, SequencerStatus},
-    sequencer::errors::ProofSenderError,
+    sequencer::{errors::ProofSenderError, utils::batch_checkpoint_name},
 };
 use aligned_sdk::{
     common::{
@@ -71,6 +75,8 @@ pub struct L1ProofSender {
     l1_chain_id: u64,
     network: Network,
     fee_estimate: FeeEstimationType,
+    /// Directory where checkpoints are stored.
+    checkpoints_dir: PathBuf,
     aligned_mode: bool,
 }
 
@@ -89,6 +95,7 @@ pub struct L1ProofSenderHealth {
 }
 
 impl L1ProofSender {
+    #[expect(clippy::too_many_arguments)]
     async fn new(
         cfg: &ProofCoordinatorConfig,
         committer_cfg: &CommitterConfig,
@@ -97,6 +104,7 @@ impl L1ProofSender {
         aligned_cfg: &AlignedConfig,
         rollup_store: StoreRollup,
         needed_proof_types: Vec<ProverType>,
+        checkpoints_dir: PathBuf,
     ) -> Result<Self, ProofSenderError> {
         let eth_client = EthClient::new_with_config(
             eth_cfg.rpc_url.clone(),
@@ -123,6 +131,7 @@ impl L1ProofSender {
             l1_chain_id,
             network: aligned_cfg.network.clone(),
             fee_estimate,
+            checkpoints_dir,
             aligned_mode: aligned_cfg.aligned_mode,
         })
     }
@@ -132,6 +141,7 @@ impl L1ProofSender {
         sequencer_state: SequencerState,
         rollup_store: StoreRollup,
         needed_proof_types: Vec<ProverType>,
+        checkpoints_dir: PathBuf,
     ) -> Result<GenServerHandle<L1ProofSender>, ProofSenderError> {
         let state = Self::new(
             &cfg.proof_coordinator,
@@ -141,6 +151,7 @@ impl L1ProofSender {
             &cfg.aligned,
             rollup_store,
             needed_proof_types,
+            checkpoints_dir,
         )
         .await?;
         let mut l1_proof_sender = L1ProofSender::start(state);
@@ -200,6 +211,20 @@ impl L1ProofSender {
             self.rollup_store
                 .set_latest_sent_batch_proof(batch_to_send)
                 .await?;
+
+            // Remove checkpoint from batch sent - 1.
+            // That checkpoint was needed to generate the proof for the batch we just sent.
+            // The checkpoint for the batch we have just sent is needed for the next batch.
+            let checkpoint_path = self
+                .checkpoints_dir
+                .join(batch_checkpoint_name(batch_to_send - 1));
+            if checkpoint_path.exists() {
+                let _ = remove_dir_all(&checkpoint_path).inspect_err(|e| {
+                    error!(
+                        "Failed to remove checkpoint directory at path {checkpoint_path:?}. Should be removed manually. Error: {e}"
+                    )
+                });
+            }
         } else {
             let missing_proof_types: Vec<String> = missing_proof_types
                 .iter()
diff --git a/crates/l2/sequencer/mod.rs b/crates/l2/sequencer/mod.rs
index 9044fdcccaf..1e696cea262 100644
--- a/crates/l2/sequencer/mod.rs
+++ b/crates/l2/sequencer/mod.rs
@@ -105,7 +105,7 @@ pub async fn start_l2(
         cfg.clone(),
         shared_state.clone(),
         genesis,
-        checkpoints_dir,
+        checkpoints_dir.clone(),
     )
     .await
     .inspect_err(|err| {
@@ -126,6 +126,7 @@ pub async fn start_l2(
         shared_state.clone(),
         rollup_store.clone(),
         needed_proof_types.clone(),
+        checkpoints_dir,
     )
     .await
     .inspect_err(|err| {
diff --git a/crates/l2/sequencer/utils.rs b/crates/l2/sequencer/utils.rs
index fa2fff1df34..0b19e610d56 100644
--- a/crates/l2/sequencer/utils.rs
+++ b/crates/l2/sequencer/utils.rs
@@ -194,3 +194,7 @@ where
 pub fn get_git_commit_hash() -> String {
     env!("VERGEN_GIT_SHA").to_string()
 }
+
+pub fn batch_checkpoint_name(batch_number: u64) -> String {
+    format!("checkpoint_batch_{batch_number}")
+}