diff --git a/storage_scrubber/src/checks.rs b/storage_scrubber/src/checks.rs
index 14788515dd..35ec69fd50 100644
--- a/storage_scrubber/src/checks.rs
+++ b/storage_scrubber/src/checks.rs
@@ -172,8 +172,11 @@ pub(crate) async fn branch_cleanup_and_check_errors(
                     }
                 }
                 BlobDataParseResult::Relic => {}
-                BlobDataParseResult::Incorrect(parse_errors) => result.errors.extend(
-                    parse_errors
+                BlobDataParseResult::Incorrect {
+                    errors,
+                    s3_layers: _,
+                } => result.errors.extend(
+                    errors
                         .into_iter()
                         .map(|error| format!("parse error: {error}")),
                 ),
@@ -300,7 +303,10 @@ pub(crate) enum BlobDataParseResult {
     },
     /// The remains of a deleted Timeline (i.e. an initdb archive only)
     Relic,
-    Incorrect(Vec<String>),
+    Incorrect {
+        errors: Vec<String>,
+        s3_layers: HashSet<(LayerName, Generation)>,
+    },
 }
 
 pub(crate) fn parse_layer_object_name(name: &str) -> Result<(LayerName, Generation), String> {
@@ -443,7 +449,7 @@ pub(crate) async fn list_timeline_blobs(
     }
 
     Ok(S3TimelineBlobData {
-        blob_data: BlobDataParseResult::Incorrect(errors),
+        blob_data: BlobDataParseResult::Incorrect { errors, s3_layers },
         unused_index_keys: index_part_keys,
         unknown_keys,
     })
diff --git a/storage_scrubber/src/main.rs b/storage_scrubber/src/main.rs
index a111c31844..cbc836755a 100644
--- a/storage_scrubber/src/main.rs
+++ b/storage_scrubber/src/main.rs
@@ -208,21 +208,21 @@ async fn main() -> anyhow::Result<()> {
                         }
 
                         if summary.is_fatal() {
-                            Err(anyhow::anyhow!("Fatal scrub errors detected"))
+                            tracing::error!("Fatal scrub errors detected");
                         } else if summary.is_empty() {
                             // Strictly speaking an empty bucket is a valid bucket, but if someone ran the
                             // scrubber they were likely expecting to scan something, and if we see no timelines
                             // at all then it's likely due to some configuration issues like a bad prefix
-                            Err(anyhow::anyhow!(
+                            tracing::error!(
                                 "No timelines found in bucket {} prefix {}",
                                 bucket_config.bucket,
                                 bucket_config
                                     .prefix_in_bucket
                                     .unwrap_or("<none>".to_string())
-                            ))
-                        } else {
-                            Ok(())
+                            );
                         }
+
+                        Ok(())
                     }
                 }
             }
diff --git a/storage_scrubber/src/pageserver_physical_gc.rs b/storage_scrubber/src/pageserver_physical_gc.rs
index 69896caa82..ff230feae3 100644
--- a/storage_scrubber/src/pageserver_physical_gc.rs
+++ b/storage_scrubber/src/pageserver_physical_gc.rs
@@ -389,10 +389,13 @@ async fn gc_ancestor(
                 // Post-deletion tenant location: don't try and GC it.
                 continue;
             }
-            BlobDataParseResult::Incorrect(reasons) => {
+            BlobDataParseResult::Incorrect {
+                errors,
+                s3_layers: _, // TODO(yuchen): could still check references to these s3 layers?
+            } => {
                 // Our primary purpose isn't to report on bad data, but log this rather than skipping silently
                 tracing::warn!(
-                    "Skipping ancestor GC for timeline {ttid}, bad metadata: {reasons:?}"
+                    "Skipping ancestor GC for timeline {ttid}, bad metadata: {errors:?}"
                 );
                 continue;
             }
@@ -518,9 +521,12 @@ pub async fn pageserver_physical_gc(
                 // Post-deletion tenant location: don't try and GC it.
                 return Ok(summary);
             }
-            BlobDataParseResult::Incorrect(reasons) => {
+            BlobDataParseResult::Incorrect {
+                errors,
+                s3_layers: _,
+            } => {
                 // Our primary purpose isn't to report on bad data, but log this rather than skipping silently
-                tracing::warn!("Skipping timeline {ttid}, bad metadata: {reasons:?}");
+                tracing::warn!("Skipping timeline {ttid}, bad metadata: {errors:?}");
                 return Ok(summary);
             }
         };
diff --git a/storage_scrubber/src/scan_pageserver_metadata.rs b/storage_scrubber/src/scan_pageserver_metadata.rs
index dc410bde41..b9630056e1 100644
--- a/storage_scrubber/src/scan_pageserver_metadata.rs
+++ b/storage_scrubber/src/scan_pageserver_metadata.rs
@@ -290,13 +290,21 @@ pub async fn scan_metadata(
             }
         }
 
-        if let BlobDataParseResult::Parsed {
-            index_part: _index_part,
-            index_part_generation: _index_part_generation,
-            s3_layers,
-        } = &data.blob_data
-        {
-            tenant_objects.push(ttid, s3_layers.clone());
+        match &data.blob_data {
+            BlobDataParseResult::Parsed {
+                index_part: _index_part,
+                index_part_generation: _index_part_generation,
+                s3_layers,
+            } => {
+                tenant_objects.push(ttid, s3_layers.clone());
+            }
+            BlobDataParseResult::Relic => (),
+            BlobDataParseResult::Incorrect {
+                errors: _,
+                s3_layers,
+            } => {
+                tenant_objects.push(ttid, s3_layers.clone());
+            }
         }
         tenant_timeline_results.push((ttid, data));
     }
diff --git a/storage_scrubber/src/tenant_snapshot.rs b/storage_scrubber/src/tenant_snapshot.rs
index 5a75f8d40e..1866e6ec80 100644
--- a/storage_scrubber/src/tenant_snapshot.rs
+++ b/storage_scrubber/src/tenant_snapshot.rs
@@ -269,7 +269,7 @@ impl SnapshotDownloader {
                         .context("Downloading timeline")?;
                     }
                     BlobDataParseResult::Relic => {}
-                    BlobDataParseResult::Incorrect(_) => {
+                    BlobDataParseResult::Incorrect { .. } => {
                         tracing::error!("Bad metadata in timeline {ttid}");
                     }
                 };
diff --git a/test_runner/fixtures/neon_fixtures.py b/test_runner/fixtures/neon_fixtures.py
index 7289472de2..c6f4404784 100644
--- a/test_runner/fixtures/neon_fixtures.py
+++ b/test_runner/fixtures/neon_fixtures.py
@@ -978,7 +978,10 @@ class NeonEnvBuilder:
                 and self.enable_scrub_on_exit
             ):
                 try:
-                    self.env.storage_scrubber.scan_metadata()
+                    healthy, _ = self.env.storage_scrubber.scan_metadata()
+                    if not healthy:
+                        e = Exception("Remote storage metadata corrupted")
+                        cleanup_error = e
                 except Exception as e:
                     log.error(f"Error during remote storage scrub: {e}")
                     cleanup_error = e
@@ -4411,14 +4414,19 @@ class StorageScrubber:
         assert stdout is not None
         return stdout
 
-    def scan_metadata(self, post_to_storage_controller: bool = False) -> Any:
+    def scan_metadata(self, post_to_storage_controller: bool = False) -> Tuple[bool, Any]:
+        """
+        Returns the health status and the metadata summary.
+        """
         args = ["scan-metadata", "--node-kind", "pageserver", "--json"]
         if post_to_storage_controller:
             args.append("--post")
         stdout = self.scrubber_cli(args, timeout=30)
 
         try:
-            return json.loads(stdout)
+            summary = json.loads(stdout)
+            healthy = not summary["with_errors"] and not summary["with_warnings"]
+            return healthy, summary
         except:
             log.error("Failed to decode JSON output from `scan-metadata`.  Dumping stdout:")
             log.error(stdout)
diff --git a/test_runner/regress/test_compatibility.py b/test_runner/regress/test_compatibility.py
index 137b0e931d..afa5f6873c 100644
--- a/test_runner/regress/test_compatibility.py
+++ b/test_runner/regress/test_compatibility.py
@@ -496,11 +496,10 @@ def test_historic_storage_formats(
     # Check the scrubber handles this old data correctly (can read it and doesn't consider it corrupt)
     #
     # Do this _before_ importing to the pageserver, as that import may start writing immediately
-    metadata_summary = env.storage_scrubber.scan_metadata()
+    healthy, metadata_summary = env.storage_scrubber.scan_metadata()
+    assert healthy
     assert metadata_summary["tenant_count"] >= 1
     assert metadata_summary["timeline_count"] >= 1
-    assert not metadata_summary["with_errors"]
-    assert not metadata_summary["with_warnings"]
 
     env.neon_cli.import_tenant(dataset.tenant_id)
 
diff --git a/test_runner/regress/test_pageserver_generations.py b/test_runner/regress/test_pageserver_generations.py
index 8941ddd281..73af7950f1 100644
--- a/test_runner/regress/test_pageserver_generations.py
+++ b/test_runner/regress/test_pageserver_generations.py
@@ -214,12 +214,11 @@ def test_generations_upgrade(neon_env_builder: NeonEnvBuilder):
 
     # Having written a mixture of generation-aware and legacy index_part.json,
     # ensure the scrubber handles the situation as expected.
-    metadata_summary = env.storage_scrubber.scan_metadata()
+    healthy, metadata_summary = env.storage_scrubber.scan_metadata()
     assert metadata_summary["tenant_count"] == 1  # Scrubber should have seen our timeline
     assert metadata_summary["timeline_count"] == 1
     assert metadata_summary["timeline_shard_count"] == 1
-    assert not metadata_summary["with_errors"]
-    assert not metadata_summary["with_warnings"]
+    assert healthy
 
 
 def test_deferred_deletion(neon_env_builder: NeonEnvBuilder):
diff --git a/test_runner/regress/test_pageserver_secondary.py b/test_runner/regress/test_pageserver_secondary.py
index 4b0af24480..8746b88a75 100644
--- a/test_runner/regress/test_pageserver_secondary.py
+++ b/test_runner/regress/test_pageserver_secondary.py
@@ -593,7 +593,8 @@ def test_secondary_downloads(neon_env_builder: NeonEnvBuilder):
     # Scrub the remote storage
     # ========================
     # This confirms that the scrubber isn't upset by the presence of the heatmap
-    env.storage_scrubber.scan_metadata()
+    healthy, _ = env.storage_scrubber.scan_metadata()
+    assert healthy
 
     # Detach secondary and delete tenant
     # ===================================
diff --git a/test_runner/regress/test_sharding.py b/test_runner/regress/test_sharding.py
index 7f30b2d7a7..1011a6fd22 100644
--- a/test_runner/regress/test_sharding.py
+++ b/test_runner/regress/test_sharding.py
@@ -124,7 +124,8 @@ def test_sharding_smoke(
 
     # Check the scrubber isn't confused by sharded content, then disable
     # it during teardown because we'll have deleted by then
-    env.storage_scrubber.scan_metadata()
+    healthy, _ = env.storage_scrubber.scan_metadata()
+    assert healthy
 
     env.storage_controller.pageserver_api().tenant_delete(tenant_id)
     assert_prefix_empty(
diff --git a/test_runner/regress/test_storage_scrubber.py b/test_runner/regress/test_storage_scrubber.py
index e3f627b6a6..388f6a9e92 100644
--- a/test_runner/regress/test_storage_scrubber.py
+++ b/test_runner/regress/test_storage_scrubber.py
@@ -516,9 +516,8 @@ def test_scrubber_scan_pageserver_metadata(
     assert len(index.layer_metadata) > 0
     it = iter(index.layer_metadata.items())
 
-    scan_summary = env.storage_scrubber.scan_metadata(post_to_storage_controller=True)
-    assert not scan_summary["with_warnings"]
-    assert not scan_summary["with_errors"]
+    healthy, scan_summary = env.storage_scrubber.scan_metadata(post_to_storage_controller=True)
+    assert healthy
 
     assert env.storage_controller.metadata_health_is_healthy()
 
@@ -532,16 +531,18 @@ def test_scrubber_scan_pageserver_metadata(
     log.info(f"delete response: {delete_response}")
 
     # Check scan summary without posting to storage controller. Expect it to be a L0 layer so only emit warnings.
-    scan_summary = env.storage_scrubber.scan_metadata()
+    _, scan_summary = env.storage_scrubber.scan_metadata()
     log.info(f"{pprint.pformat(scan_summary)}")
     assert len(scan_summary["with_warnings"]) > 0
 
     assert env.storage_controller.metadata_health_is_healthy()
 
     # Now post to storage controller, expect seeing one unhealthy health record
-    scan_summary = env.storage_scrubber.scan_metadata(post_to_storage_controller=True)
+    _, scan_summary = env.storage_scrubber.scan_metadata(post_to_storage_controller=True)
     log.info(f"{pprint.pformat(scan_summary)}")
     assert len(scan_summary["with_warnings"]) > 0
 
     unhealthy = env.storage_controller.metadata_health_list_unhealthy()["unhealthy_tenant_shards"]
     assert len(unhealthy) == 1 and unhealthy[0] == str(tenant_shard_id)
+
+    neon_env_builder.disable_scrub_on_exit()
diff --git a/test_runner/regress/test_tenant_delete.py b/test_runner/regress/test_tenant_delete.py
index c343b349cf..c01b3a2e89 100644
--- a/test_runner/regress/test_tenant_delete.py
+++ b/test_runner/regress/test_tenant_delete.py
@@ -341,13 +341,13 @@ def test_tenant_delete_scrubber(pg_bin: PgBin, neon_env_builder: NeonEnvBuilder)
     wait_for_upload(ps_http, tenant_id, timeline_id, last_flush_lsn)
     env.stop()
 
-    result = env.storage_scrubber.scan_metadata()
-    assert result["with_warnings"] == []
+    healthy, _ = env.storage_scrubber.scan_metadata()
+    assert healthy
 
     env.start()
     ps_http = env.pageserver.http_client()
     ps_http.tenant_delete(tenant_id)
     env.stop()
 
-    env.storage_scrubber.scan_metadata()
-    assert result["with_warnings"] == []
+    healthy, _ = env.storage_scrubber.scan_metadata()
+    assert healthy