diff --git a/sdk/python/feast/infra/registry/registry.py b/sdk/python/feast/infra/registry/registry.py
index 76da6ad831d..f3437b08f30 100644
--- a/sdk/python/feast/infra/registry/registry.py
+++ b/sdk/python/feast/infra/registry/registry.py
@@ -386,6 +386,12 @@ def list_data_sources(
     def apply_data_source(
         self, data_source: DataSource, project: str, commit: bool = True
     ):
+        """Apply a data source to the registry with project-scoped deduplication.
+
+        Filters existing data sources by both name and project (fixes feast-dev/feast#6206),
+        preserving the original created_timestamp if the source already exists in the
+        target project.
+        """
         now = _utc_now()
         if not data_source.created_timestamp:
             data_source.created_timestamp = now
@@ -394,7 +400,10 @@ def apply_data_source(
         registry = self._prepare_registry_for_changes(project)
 
         for idx, existing_data_source_proto in enumerate(registry.data_sources):
-            if existing_data_source_proto.name == data_source.name:
+            if (
+                existing_data_source_proto.name == data_source.name
+                and existing_data_source_proto.project == project
+            ):
                 existing_data_source = DataSource.from_proto(existing_data_source_proto)
                 # Check if the data source has actually changed
                 if existing_data_source == data_source:
@@ -423,7 +432,7 @@ def delete_data_source(self, name: str, project: str, commit: bool = True):
         for idx, data_source_proto in enumerate(
             self.cached_registry_proto.data_sources
         ):
-            if data_source_proto.name == name:
+            if data_source_proto.name == name and data_source_proto.project == project:
                 del self.cached_registry_proto.data_sources[idx]
                 if commit:
                     self.commit()
diff --git a/sdk/python/tests/integration/registration/test_universal_registry.py b/sdk/python/tests/integration/registration/test_universal_registry.py
index fb09395d789..88d827d786a 100644
--- a/sdk/python/tests/integration/registration/test_universal_registry.py
+++ b/sdk/python/tests/integration/registration/test_universal_registry.py
@@ -899,6 +899,111 @@ def test_apply_data_source_with_timestamps(test_registry):
     test_registry.teardown()
 
 
+@pytest.mark.integration
+@pytest.mark.parametrize(
+    "test_registry",
+    all_fixtures,
+)
+def test_apply_data_source_cross_project_isolation(test_registry):
+    """Test that apply_data_source uses project-scoped filtering.
+
+    Regression test for https://github.com/feast-dev/feast/issues/6206:
+    applying a data source to one project must not overwrite the data source
+    with the same name in a different project.
+
+    See: feast-dev/feast#6298
+    """
+    project_a = "project_a"
+    project_b = "project_b"
+
+    source_a = FileSource(
+        name="shared_source_name",
+        file_format=ParquetFormat(),
+        path="file://feast/project_a.parquet",
+        timestamp_field="ts_col",
+    )
+    source_b = FileSource(
+        name="shared_source_name",
+        file_format=ParquetFormat(),
+        path="file://feast/project_b.parquet",
+        timestamp_field="ts_col",
+    )
+
+    test_registry.apply_data_source(source_a, project_a, commit=True)
+    test_registry.apply_data_source(source_b, project_b, commit=True)
+
+    # Each project should have exactly its own source
+    sources_a = test_registry.list_data_sources(project_a)
+    sources_b = test_registry.list_data_sources(project_b)
+    assert len(sources_a) == 1
+    assert len(sources_b) == 1
+
+    # Paths must be project-specific — not overwritten cross-project
+    assert sources_a[0].path == "file://feast/project_a.parquet"
+    assert sources_b[0].path == "file://feast/project_b.parquet"
+
+    # Re-apply source_b with updated path: must not bleed into project_a
+    source_b_updated = FileSource(
+        name="shared_source_name",
+        file_format=ParquetFormat(),
+        path="file://feast/project_b_v2.parquet",
+        timestamp_field="ts_col",
+    )
+    test_registry.apply_data_source(source_b_updated, project_b, commit=True)
+
+    sources_a_after = test_registry.list_data_sources(project_a)
+    assert len(sources_a_after) == 1
+    assert sources_a_after[0].path == "file://feast/project_a.parquet", (
+        "apply_data_source for project_b must not overwrite project_a's source"
+    )
+
+    test_registry.teardown()
+
+
+@pytest.mark.integration
+@pytest.mark.parametrize(
+    "test_registry",
+    all_fixtures,
+)
+def test_delete_data_source_project_scoped(test_registry):
+    """Test that delete_data_source only removes the source from the given project.
+
+    Regression test for https://github.com/feast-dev/feast/issues/6206:
+    deleting a data source from one project must not delete the data source
+    with the same name from another project.
+    """
+    project_a = "project_a"
+    project_b = "project_b"
+
+    source_a = FileSource(
+        name="shared_source_name",
+        file_format=ParquetFormat(),
+        path="file://feast/project_a.parquet",
+        timestamp_field="ts_col",
+    )
+    source_b = FileSource(
+        name="shared_source_name",
+        file_format=ParquetFormat(),
+        path="file://feast/project_b.parquet",
+        timestamp_field="ts_col",
+    )
+
+    test_registry.apply_data_source(source_a, project_a, commit=True)
+    test_registry.apply_data_source(source_b, project_b, commit=True)
+
+    # Delete the source from project_a only
+    test_registry.delete_data_source("shared_source_name", project_a, commit=True)
+
+    # project_a should have no sources; project_b should be unaffected
+    sources_a = test_registry.list_data_sources(project_a)
+    sources_b = test_registry.list_data_sources(project_b)
+    assert len(sources_a) == 0, "Source should be deleted from project_a"
+    assert len(sources_b) == 1, "Source in project_b must not be deleted"
+    assert sources_b[0].path == "file://feast/project_b.parquet"
+
+    test_registry.teardown()
+
+
 @pytest.mark.integration
 @pytest.mark.parametrize(
     "test_registry",