diff --git a/pageserver/src/tenant/remote_timeline_client.rs b/pageserver/src/tenant/remote_timeline_client.rs
index 7d6f7e8d39..e46205810a 100644
--- a/pageserver/src/tenant/remote_timeline_client.rs
+++ b/pageserver/src/tenant/remote_timeline_client.rs
@@ -651,8 +651,9 @@ impl RemoteTimelineClient {
         // to syntactically forbid ? or bail! calls here.
         let no_bail_here = || {
             for name in names {
-                upload_queue.latest_files.remove(name);
-                upload_queue.latest_files_changes_since_metadata_upload_scheduled += 1;
+                if upload_queue.latest_files.remove(name).is_some() {
+                    upload_queue.latest_files_changes_since_metadata_upload_scheduled += 1;
+                }
             }
 
             if upload_queue.latest_files_changes_since_metadata_upload_scheduled > 0 {
diff --git a/pageserver/src/tenant/timeline.rs b/pageserver/src/tenant/timeline.rs
index 6245c639dd..ddf6f0bc0a 100644
--- a/pageserver/src/tenant/timeline.rs
+++ b/pageserver/src/tenant/timeline.rs
@@ -1614,7 +1614,7 @@ impl Timeline {
         let (conf, tenant_id, timeline_id) = (self.conf, self.tenant_id, self.timeline_id);
         let span = tracing::Span::current();
 
-        let (loaded_layers, needs_upload, total_physical_size) = tokio::task::spawn_blocking({
+        let (loaded_layers, to_sync, total_physical_size) = tokio::task::spawn_blocking({
             move || {
                 let _g = span.entered();
                 let discovered = init::scan_timeline_dir(&timeline_path)?;
@@ -1660,6 +1660,7 @@ impl Timeline {
 
                 let mut loaded_layers = Vec::new();
                 let mut needs_upload = Vec::new();
+                let mut needs_cleanup = Vec::new();
                 let mut total_physical_size = 0;
 
                 for (name, decision) in decided {
@@ -1675,14 +1676,10 @@ impl Timeline {
                         Err(FutureLayer { local }) => {
                             if local.is_some() {
                                 path.push(name.file_name());
-                                init::cleanup_future_layer(&path, name, disk_consistent_lsn)?;
+                                init::cleanup_future_layer(&path, &name, disk_consistent_lsn)?;
                                 path.pop();
-                            } else {
-                                // we cannot do anything for remote layers, but not continuing to
-                                // process it will leave it out index_part.json as well.
                             }
-                            //
-                            // we do not currently schedule deletions for these.
+                            needs_cleanup.push(name);
                             continue;
                         }
                     };
@@ -1736,7 +1733,11 @@ impl Timeline {
 
                     loaded_layers.push(layer);
                 }
-                Ok((loaded_layers, needs_upload, total_physical_size))
+                Ok((
+                    loaded_layers,
+                    (needs_upload, needs_cleanup),
+                    total_physical_size,
+                ))
             }
         })
         .await
@@ -1748,9 +1749,11 @@ impl Timeline {
         guard.initialize_local_layers(loaded_layers, disk_consistent_lsn + 1);
 
         if let Some(rtc) = self.remote_client.as_ref() {
+            let (needs_upload, needs_cleanup) = to_sync;
             for (layer, m) in needs_upload {
                 rtc.schedule_layer_file_upload(&layer.layer_desc().filename(), &m)?;
             }
+            rtc.schedule_layer_file_deletion(&needs_cleanup)?;
             rtc.schedule_index_upload_for_file_changes()?;
             // Tenant::create_timeline will wait for these uploads to happen before returning, or
             // on retry.
diff --git a/pageserver/src/tenant/timeline/init.rs b/pageserver/src/tenant/timeline/init.rs
index cdd4227b44..a270d96677 100644
--- a/pageserver/src/tenant/timeline/init.rs
+++ b/pageserver/src/tenant/timeline/init.rs
@@ -183,7 +183,7 @@ pub(super) fn cleanup_local_file_for_remote(
 
 pub(super) fn cleanup_future_layer(
     path: &Path,
-    name: LayerFileName,
+    name: &LayerFileName,
     disk_consistent_lsn: Lsn,
 ) -> anyhow::Result<()> {
     use LayerFileName::*;