diff --git a/nmdc_runtime/site/graphs.py b/nmdc_runtime/site/graphs.py
index 1d2a655c4..5e51241cf 100644
--- a/nmdc_runtime/site/graphs.py
+++ b/nmdc_runtime/site/graphs.py
@@ -126,6 +126,9 @@ def apply_changesheet():
 
 @graph
 def apply_metadata_in():
+    """
+    TODO: Document this function.
+    """
     # Note: We use `_` as a "placeholder" variable.
     outputs = perform_mongo_updates(get_json_in())
     _ = add_output_run_event(outputs)
diff --git a/nmdc_runtime/site/ops.py b/nmdc_runtime/site/ops.py
index 710c67e78..7f6484f34 100644
--- a/nmdc_runtime/site/ops.py
+++ b/nmdc_runtime/site/ops.py
@@ -380,6 +380,9 @@ def get_json_in(context):
 
 @op(required_resource_keys={"runtime_api_site_client", "mongo"})
 def perform_mongo_updates(context, json_in):
+    """
+    TODO: Document this function.
+    """
     mongo = context.resources.mongo
     client: RuntimeApiSiteClient = context.resources.runtime_api_site_client
     op_id = context.op_config.get("operation_id")
@@ -389,7 +392,9 @@ def perform_mongo_updates(context, json_in):
     context.log.debug(f"{docs}")
 
     rv = validate_json(
-        docs, mongo.db
+        docs,
+        mongo.db,
+        check_inter_document_references=True,
     )  # use *exact* same check as /metadata/json:validate
     if rv["result"] == "errors":
         raise Failure(str(rv["detail"]))
diff --git a/tests/test_ops/test_ops.py b/tests/test_ops/test_ops.py
index 3c0d428c1..c673a095b 100644
--- a/tests/test_ops/test_ops.py
+++ b/tests/test_ops/test_ops.py
@@ -12,6 +12,7 @@
 )
 
 from nmdc_runtime.site.graphs import apply_metadata_in
+from tests.lib.faker import Faker
 
 
 @pytest.fixture
@@ -46,17 +47,30 @@ def op_context():
 
 
 def test_apply_metadata_in_functional_annotation_agg(op_context):
-    mongo = op_context.resources.mongo
+    db = op_context.resources.mongo.db  # concise alias
+    
+    # Insert the _referenced_ document first, so that referential integrity is maintained.
+    faker = Faker()
+    workflow_execution_id = "nmdc:wfmtan-13-hemh0a82.1"
+    workflow_execution: dict = faker.generate_metagenome_annotations(
+        1,
+        was_informed_by=['nmdc:dgns-00-000001'],
+        has_input=['nmdc:bsm-00-000001']
+    )[0]
+    workflow_execution["id"] = workflow_execution_id
+    assert db.workflow_execution.count_documents({"id": workflow_execution_id}) == 0
+    db.workflow_execution_set.insert_one(workflow_execution)
+
     docs = {
         "functional_annotation_agg": [
             {
-                "was_generated_by": "nmdc:wfmtan-13-hemh0a82.1",
+                "was_generated_by": workflow_execution_id,
                 "gene_function_id": "KEGG.ORTHOLOGY:K00005",
                 "count": 10,
                 "type": "nmdc:FunctionalAnnotationAggMember",
             },
             {
-                "was_generated_by": "nmdc:wfmtan-13-hemh0a82.1",
+                "was_generated_by": workflow_execution_id,
                 "gene_function_id": "KEGG.ORTHOLOGY:K01426",
                 "count": 5,
                 "type": "nmdc:FunctionalAnnotationAggMember",
@@ -65,12 +79,12 @@ def test_apply_metadata_in_functional_annotation_agg(op_context):
     }
     # Ensure the docs are not already in the test database.
     for doc_spec in docs["functional_annotation_agg"]:
-        mongo.db.functional_annotation_agg.delete_many(doc_spec)
+        db.functional_annotation_agg.delete_many(doc_spec)
 
     extra_run_config_data = _ensure_job__metadata_in(
         docs,
         op_context.resources.runtime_api_user_client.username,
-        mongo.db,
+        db,
         op_context.resources.runtime_api_site_client.client_id,
         drs_object_exists_ok=True,  # If there exists a DRS object with a matching checksum, use it.
     )
@@ -80,8 +94,55 @@ def test_apply_metadata_in_functional_annotation_agg(op_context):
     )
 
     assert (
-        mongo.db.functional_annotation_agg.count_documents(
+        db.functional_annotation_agg.count_documents(
             {"$or": docs["functional_annotation_agg"]}
         )
         == 2
     )
+
+    # 🧹 Clean up the test database.
+    db.workflow_execution_set.delete_many({"id": workflow_execution_id})
+    for doc_spec in docs["functional_annotation_agg"]:
+        db.functional_annotation_agg.delete_many(doc_spec)
+
+
+def test_apply_metadata_in_checks_referential_integrity(op_context):
+    db = op_context.resources.mongo.db  # concise alias
+    
+    # Confirm the _referenced_ document does not exist (anywhere the schema says it can).
+    workflow_execution_id = "nmdc:wfmtan-00-000000.1"
+    assert db.workflow_execution_set.count_documents({"id": workflow_execution_id}) == 0
+
+    functional_annotation_agg_member = {
+        "was_generated_by": workflow_execution_id,
+        "gene_function_id": "KEGG.ORTHOLOGY:K00005",
+        "count": 10,
+        "type": "nmdc:FunctionalAnnotationAggMember",
+    }
+
+    docs = {"functional_annotation_agg": [functional_annotation_agg_member]}
+
+    # Confirm the `functional_annotation_agg` document does not exist.
+    assert db.functional_annotation_agg.count_documents(
+        functional_annotation_agg_member
+    ) == 0
+
+    # Note: This statement was copied from the `test_apply_metadata_in_functional_annotation_agg` test above.
+    extra_run_config_data = _ensure_job__metadata_in(
+        docs,
+        op_context.resources.runtime_api_user_client.username,
+        db,
+        op_context.resources.runtime_api_site_client.client_id,
+        drs_object_exists_ok=True,  # If there exists a DRS object with a matching checksum, use it.
+    )
+
+    with pytest.raises(Exception) as exc_info:
+        apply_metadata_in.to_job(**preset_normal).execute_in_process(
+            run_config=extra_run_config_data
+        )
+        assert "references" in str(exc_info.value)
+
+    # Confirm the `functional_annotation_agg` document _still_ does not exist.
+    assert db.functional_annotation_agg.count_documents(
+        functional_annotation_agg_member
+    ) == 0