diff --git a/pageserver/src/tenant/timeline.rs b/pageserver/src/tenant/timeline.rs
index d437724673..b4d908b130 100644
--- a/pageserver/src/tenant/timeline.rs
+++ b/pageserver/src/tenant/timeline.rs
@@ -4540,7 +4540,12 @@ impl Timeline {
         new_images: &[ResidentLayer],
         layers_to_remove: &[Layer],
     ) -> Result<(), CompactionError> {
-        let mut guard = self.layers.write().await;
+        let mut guard = tokio::select! {
+            guard = self.layers.write() => guard,
+            _ = self.cancel.cancelled() => {
+                return Err(CompactionError::ShuttingDown);
+            }
+        };
 
         let mut duplicated_layers = HashSet::new();
 
diff --git a/pageserver/src/tenant/timeline/compaction.rs b/pageserver/src/tenant/timeline/compaction.rs
index e24459e7b9..7370ec1386 100644
--- a/pageserver/src/tenant/timeline/compaction.rs
+++ b/pageserver/src/tenant/timeline/compaction.rs
@@ -1048,11 +1048,22 @@ impl Timeline {
         let mut dup_end_lsn: Lsn = Lsn::INVALID; // end LSN of layer containing values of the single key
         let mut next_hole = 0; // index of next hole in holes vector
 
+        let mut keys = 0;
+
         while let Some((key, lsn, value)) = all_values_iter
             .next(ctx)
             .await
             .map_err(CompactionError::Other)?
         {
+            keys += 1;
+
+            if keys % 32_768 == 0 && self.cancel.is_cancelled() {
+                // avoid hitting the cancellation token on every key. in benches, we end up
+                // shuffling an order of million keys per layer, this means we'll check it
+                // around tens of times per layer.
+                return Err(CompactionError::ShuttingDown);
+            }
+
             let same_key = prev_key.map_or(false, |prev_key| prev_key == key);
             // We need to check key boundaries once we reach next key or end of layer with the same key
             if !same_key || lsn == dup_end_lsn {
@@ -1157,6 +1168,8 @@ impl Timeline {
                         .await
                         .map_err(CompactionError::Other)?,
                     );
+
+                    keys = 0;
                 }
 
                 writer