diff --git a/test_runner/regress/test_remote_storage.py b/test_runner/regress/test_remote_storage.py
index 298aae39ee..8975a437dc 100644
--- a/test_runner/regress/test_remote_storage.py
+++ b/test_runner/regress/test_remote_storage.py
@@ -621,6 +621,7 @@ def test_timeline_deletion_with_files_stuck_in_upload_queue(
         path
         for path in remote_timeline_path.iterdir()
         if not (path.name.endswith("initdb.tar.zst"))
+        and not (path.name.startswith("index_part.json"))
     ]
     assert len(filtered) == 0
 
diff --git a/test_runner/regress/test_storage_scrubber.py b/test_runner/regress/test_storage_scrubber.py
index e29cb801d5..8f8b6ccd96 100644
--- a/test_runner/regress/test_storage_scrubber.py
+++ b/test_runner/regress/test_storage_scrubber.py
@@ -410,6 +410,7 @@ def test_scrubber_physical_gc_timeline_deletion(neon_env_builder: NeonEnvBuilder
 
     # Delete the timeline
     env.storage_controller.pageserver_api().timeline_delete(tenant_id, timeline_id)
+    time.sleep(1)  # give scrubber some time to wait for min_age_secs
 
     # Subsequently doing physical GC should clean up the ancestor layers
     gc_summary = env.storage_scrubber.pageserver_physical_gc(min_age_secs=0, mode="full")
diff --git a/test_runner/regress/test_timeline_archive.py b/test_runner/regress/test_timeline_archive.py
index 41286a2adc..d19b4f4113 100644
--- a/test_runner/regress/test_timeline_archive.py
+++ b/test_runner/regress/test_timeline_archive.py
@@ -491,7 +491,7 @@ def test_timeline_archival_chaos(neon_env_builder: NeonEnvBuilder):
 
         return (active_ids, offloaded_ids)
 
-    def timeline_objects(tenant_shard_id, timeline_id):
+    def timeline_objects_exclude_index_part(tenant_shard_id, timeline_id):
         response = list_prefix(
             env.pageserver_remote_storage,  # type: ignore
             prefix="/".join(
@@ -505,7 +505,11 @@ def test_timeline_archival_chaos(neon_env_builder: NeonEnvBuilder):
             + "/",
         )
 
-        return [k["Key"] for k in response.get("Contents", [])]
+        return [
+            k["Key"]
+            for k in response.get("Contents", [])
+            if not k["Key"].startswith("index_part.json")
+        ]
 
     def worker():
         """
@@ -533,7 +537,7 @@ def test_timeline_archival_chaos(neon_env_builder: NeonEnvBuilder):
                     state.created = True
 
                     if (
-                        timeline_objects(
+                        timeline_objects_exclude_index_part(
                             tenant_shard_id=tenant_shard_id, timeline_id=state.timeline_id
                         )
                         == []
@@ -550,7 +554,9 @@ def test_timeline_archival_chaos(neon_env_builder: NeonEnvBuilder):
                         violations.append(msg)
                         raise RuntimeError(msg)
 
-                    objects = timeline_objects(tenant_shard_id, state.timeline_id)
+                    objects = timeline_objects_exclude_index_part(
+                        tenant_shard_id, state.timeline_id
+                    )
                     if len(objects) == 0:
                         log.info(f"Confirmed deletion of timeline {state.timeline_id}")
                         timelines_deleted.append(state.timeline_id)