diff --git a/src/datasets/utils/metadata.py b/src/datasets/utils/metadata.py
index 809b8dc07dc..b2d4f93618a 100644
--- a/src/datasets/utils/metadata.py
+++ b/src/datasets/utils/metadata.py
@@ -175,6 +175,10 @@ def from_yaml_string(cls, string: str) -> "DatasetMetadata":
             :obj:`TypeError`: If the dataset's metadata is invalid
         """
         metada_dict = yaml.safe_load(string) or dict()
+        # flatten the metadata of each config
+        for key in metada_dict:
+            if isinstance(metada_dict[key], dict):
+                metada_dict[key] = list(set(sum(metada_dict[key].values(), [])))
         return cls(**metada_dict)
 
     @staticmethod
diff --git a/tests/test_metadata_util.py b/tests/test_metadata_util.py
index a24e0741862..a5b4c4257b1 100644
--- a/tests/test_metadata_util.py
+++ b/tests/test_metadata_util.py
@@ -1,3 +1,4 @@
+import re
 import tempfile
 import unittest
 from pathlib import Path
@@ -13,7 +14,8 @@
 
 
 def _dedent(string: str) -> str:
-    return "\n".join([line.lstrip() for line in string.splitlines()])
+    indent_level = min(re.search("^ +", t).end() if t.startswith(" ") else 0 for t in string.splitlines())
+    return "\n".join([line[indent_level:] for line in string.splitlines()])
 
 
 README_YAML = """\
@@ -187,6 +189,33 @@ def test_from_yaml_string(self):
         )
         DatasetMetadata.from_yaml_string(valid_yaml_string)
 
+        valid_yaml_string_with_configs = _dedent(
+            """\
+            annotations_creators:
+            - found
+            language_creators:
+            - found
+            languages:
+              en:
+              - en
+              fr:
+              - fr
+            licenses:
+            - unknown
+            multilinguality:
+            - monolingual
+            size_categories:
+            - 10K<n<100K
+            source_datasets:
+            - extended|other-yahoo-webscope-l6
+            task_categories:
+            - question-answering
+            task_ids:
+            - open-domain-qa
+            """
+        )
+        DatasetMetadata.from_yaml_string(valid_yaml_string_with_configs)
+
         invalid_tag_yaml = _dedent(
             """\
             annotations_creators: