diff --git a/c/tests/test_tables.c b/c/tests/test_tables.c
index 3f50b817df..f539e0744e 100644
--- a/c/tests/test_tables.c
+++ b/c/tests/test_tables.c
@@ -5074,6 +5074,8 @@ test_table_collection_union(void)
     tsk_table_collection_t tables_empty;
     tsk_table_collection_t tables_copy;
     tsk_id_t node_mapping[3];
+    char example_metadata[100] = "An example of metadata with unicode 🎄🌳🌴🌲🎋";
+    tsk_size_t example_metadata_length = (tsk_size_t) strlen(example_metadata);
 
     memset(node_mapping, 0xff, sizeof(node_mapping));
 
@@ -5087,8 +5089,14 @@ test_table_collection_union(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     // does not error on empty tables
-    ret = tsk_table_collection_union(
-        &tables, &tables_empty, node_mapping, TSK_UNION_NO_CHECK_SHARED);
+    ret = tsk_table_collection_union(&tables, &tables_empty, node_mapping, 0);
+    CU_ASSERT_EQUAL_FATAL(ret, 0);
+
+    // does not error on empty tables but that differ on top level metadata
+    ret = tsk_table_collection_set_metadata(
+        &tables, example_metadata, example_metadata_length);
+    CU_ASSERT_EQUAL(ret, 0);
+    ret = tsk_table_collection_union(&tables, &tables_empty, node_mapping, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     // three nodes, two pop, three ind, two edge, two site, two mut
diff --git a/c/tskit/tables.c b/c/tskit/tables.c
index 074386ae91..7d3fef08ba 100644
--- a/c/tskit/tables.c
+++ b/c/tskit/tables.c
@@ -9256,14 +9256,6 @@ tsk_check_subset_equality(tsk_table_collection_t *self,
     if (ret != 0) {
         goto out;
     }
-    ret = tsk_provenance_table_clear(&other_copy.provenances);
-    if (ret != 0) {
-        goto out;
-    }
-    ret = tsk_provenance_table_clear(&self_copy.provenances);
-    if (ret != 0) {
-        goto out;
-    }
     ret = tsk_table_collection_subset(&self_copy, self_nodes, num_shared_nodes);
     if (ret != 0) {
         goto out;
@@ -9272,7 +9264,8 @@ tsk_check_subset_equality(tsk_table_collection_t *self,
     if (ret != 0) {
         goto out;
     }
-    if (!tsk_table_collection_equals(&self_copy, &other_copy, 0)) {
+    if (!tsk_table_collection_equals(&self_copy, &other_copy,
+            TSK_CMP_IGNORE_TS_METADATA | TSK_CMP_IGNORE_PROVENANCE)) {
         ret = TSK_ERR_UNION_DIFF_HISTORIES;
         goto out;
     }
diff --git a/python/tests/test_tables.py b/python/tests/test_tables.py
index e790953b67..099d718513 100644
--- a/python/tests/test_tables.py
+++ b/python/tests/test_tables.py
@@ -3216,6 +3216,12 @@ def split_example(self, ts, T):
             i if i < len(shared_nodes) else tskit.NULL
             for i in range(tables2.nodes.num_rows)
         ]
+        # adding some metadata to one of the tables
+        # union should disregard differences in metadata
+        tables1.metadata_schema = tskit.MetadataSchema(
+            {"codec": "json", "type": "object"}
+        )
+        tables1.metadata = {"hello": "world"}
         return tables1, tables2, node_mapping
 
     def verify_union_equality(self, tables, other, node_mapping, add_populations=True):
@@ -3225,7 +3231,7 @@ def verify_union_equality(self, tables, other, node_mapping, add_populations=Tru
         uni1.union(
             other,
             node_mapping,
-            record_provenance=False,
+            record_provenance=True,
             add_populations=add_populations,
         )
         tsutil.py_union(
@@ -3235,15 +3241,13 @@ def verify_union_equality(self, tables, other, node_mapping, add_populations=Tru
             record_provenance=False,
             add_populations=add_populations,
         )
-        assert uni1 == uni2
+        assert uni1.equals(uni2, ignore_ts_metadata=True, ignore_provenance=True)
         # verifying that subsetting to original nodes return the same table
         orig_nodes = [j for i, j in enumerate(node_mapping) if j != tskit.NULL]
         uni1.subset(orig_nodes)
         # subsetting tables just to make sure order is the same
         tables.subset(orig_nodes)
-        uni1.provenances.clear()
-        tables.provenances.clear()
-        assert uni1 == tables
+        assert uni1.equals(tables, ignore_ts_metadata=True, ignore_provenance=True)
 
     def test_noshared_example(self):
         ts1 = self.get_msprime_example(sample_size=3, T=2, seed=9328)