diff --git a/src/tape/ensemble.py b/src/tape/ensemble.py
index 35eb7ead..00233c44 100644
--- a/src/tape/ensemble.py
+++ b/src/tape/ensemble.py
@@ -1550,8 +1550,8 @@ def _sync_tables(self):
                 # Lazily Create an empty object table (just index) for joining
                 empty_obj = self._object.map_partitions(lambda x: pd.DataFrame(index=x.index))
 
-                # Join source onto the empty object table to align
-                self._source = empty_obj.join(self._source)
+                # Join source onto the empty object table to remove IDs not present in both tables
+                self._source = self._source.join(empty_obj, how="inner")
             else:
                 warnings.warn("Divisions are not known, syncing using a non-lazy method.")
                 obj_idx = list(self._object.index.compute())
@@ -1570,8 +1570,9 @@ def _sync_tables(self):
                     # Lazily Create an empty source table (just unique indexes) for joining
                     empty_src = self._source.map_partitions(lambda x: pd.DataFrame(index=x.index.unique()))
 
-                    # Join object onto the empty unique source table to align
-                    self._object = empty_src.join(self._object)
+                    # Join object onto the empty unique source table to remove IDs not present in
+                    # both tables
+                    self._object = self._object.join(empty_src, how="inner")
 
                 else:
                     warnings.warn("Divisions are not known, syncing using a non-lazy method.")
diff --git a/tests/tape_tests/test_ensemble.py b/tests/tape_tests/test_ensemble.py
index f4bb7df2..7c8a96ba 100644
--- a/tests/tape_tests/test_ensemble.py
+++ b/tests/tape_tests/test_ensemble.py
@@ -595,16 +595,29 @@ def test_sync_tables(data_fixture, request):
     parquet_ensemble.dropna(table="source")
     assert parquet_ensemble._source_dirty  # Dropna should set the source dirty flag
 
-    # Drop a whole object to test that the object is dropped in the object table
-    parquet_ensemble.query(f"{parquet_ensemble._id_col} != 88472935274829959", table="source")
+    # Drop a whole object from Source to test that the object is dropped in the object table
+    dropped_obj_id = 88472935274829959
+    parquet_ensemble.query(f"{parquet_ensemble._id_col} != {dropped_obj_id}", table="source")
 
-    parquet_ensemble._sync_tables()
+    # Marks the Object table as dirty without triggering a sync. This is good to test since
+    # we always sync the object table first.
+    parquet_ensemble.dropna("object")
+
+    # Verify that the object ID we removed from the source table is present in the object table
+    assert dropped_obj_id in parquet_ensemble._object.index.compute().values
 
-    # both tables should have the expected number of rows after a sync
+    # Perform an operation which should trigger syncing both tables.
+    parquet_ensemble.compute()
+
+    # Both tables should have the expected number of rows after a sync
     assert len(parquet_ensemble.compute("object")) == 4
     assert len(parquet_ensemble.compute("source")) == 1063
 
-    # dirty flags should be unset after sync
+    # Validate that the filtered object has been removed from both tables.
+    assert dropped_obj_id not in parquet_ensemble._source.index.compute().values
+    assert dropped_obj_id not in parquet_ensemble._object.index.compute().values
+
+    # Dirty flags should be unset after sync
     assert not parquet_ensemble._object_dirty
     assert not parquet_ensemble._source_dirty