diff --git a/s3_scrubber/src/checks.rs b/s3_scrubber/src/checks.rs
index 510a128663..1c2bf9c8fa 100644
--- a/s3_scrubber/src/checks.rs
+++ b/s3_scrubber/src/checks.rs
@@ -170,6 +170,7 @@ pub(crate) async fn branch_cleanup_and_check_errors(
                         ));
                     }
                 }
+                BlobDataParseResult::Relic => {}
                 BlobDataParseResult::Incorrect(parse_errors) => result.errors.extend(
                     parse_errors
                         .into_iter()
@@ -215,6 +216,8 @@ pub(crate) enum BlobDataParseResult {
         index_part_generation: Generation,
         s3_layers: HashSet<(LayerFileName, Generation)>,
     },
+    /// The remains of a deleted Timeline (i.e. an initdb archive only)
+    Relic,
     Incorrect(Vec<String>),
 }
 
@@ -245,6 +248,7 @@ pub(crate) async fn list_timeline_blobs(
     timeline_dir_target.delimiter = String::new();
 
     let mut index_parts: Vec<ObjectIdentifier> = Vec::new();
+    let mut initdb_archive: bool = false;
 
     let stream = stream_listing(s3_client, &timeline_dir_target);
     pin_mut!(stream);
@@ -258,6 +262,10 @@ pub(crate) async fn list_timeline_blobs(
                 tracing::info!("Index key {key}");
                 index_parts.push(obj)
             }
+            Some("initdb.tar.zst") => {
+                tracing::info!("initdb archive {key}");
+                initdb_archive = true;
+            }
             Some(maybe_layer_name) => match parse_layer_object_name(maybe_layer_name) {
                 Ok((new_layer, gen)) => {
                     tracing::info!("Parsed layer key: {} {:?}", new_layer, gen);
@@ -279,6 +287,16 @@ pub(crate) async fn list_timeline_blobs(
         }
     }
 
+    if index_parts.is_empty() && s3_layers.is_empty() && initdb_archive {
+        tracing::info!(
+            "Timeline is empty apart from initdb archive: expected post-deletion state."
+        );
+        return Ok(S3TimelineBlobData {
+            blob_data: BlobDataParseResult::Relic,
+            keys_to_remove: Vec::new(),
+        });
+    }
+
     // Choose the index_part with the highest generation
     let (index_part_object, index_part_generation) = match index_parts
         .iter()