diff --git a/carstore/bs.go b/carstore/bs.go
index cc903ed5a..86d3cfaaa 100644
--- a/carstore/bs.go
+++ b/carstore/bs.go
@@ -91,9 +91,9 @@ type blockRef struct {
 }
 
 type staleRef struct {
-	ID  uint         `gorm:"primarykey"`
-	Cid models.DbCID `gorm:"index"`
-	Usr models.Uid
+	ID  uint `gorm:"primarykey"`
+	Cid models.DbCID
+	Usr models.Uid `gorm:"index"`
 }
 
 type userView struct {
@@ -965,36 +965,52 @@ func (cs *CarStore) deleteShards(ctx context.Context, shs []*CarShard) error {
 	ctx, span := otel.Tracer("carstore").Start(ctx, "deleteShard")
 	defer span.End()
 
-	var ids []uint
-	for _, sh := range shs {
-		ids = append(ids, sh.ID)
-	}
+	deleteSlice := func(ctx context.Context, subs []*CarShard) error {
+		var ids []uint
+		for _, sh := range subs {
+			ids = append(ids, sh.ID)
+		}
 
-	txn := cs.meta.Begin()
+		txn := cs.meta.Begin()
 
-	if err := txn.Delete(&CarShard{}, "id in (?)", ids).Error; err != nil {
-		return err
-	}
+		if err := txn.Delete(&CarShard{}, "id in (?)", ids).Error; err != nil {
+			return err
+		}
 
-	if err := txn.Delete(&blockRef{}, "shard in (?)", ids).Error; err != nil {
-		return err
-	}
+		if err := txn.Delete(&blockRef{}, "shard in (?)", ids).Error; err != nil {
+			return err
+		}
 
-	if err := txn.Commit().Error; err != nil {
-		return err
-	}
+		if err := txn.Commit().Error; err != nil {
+			return err
+		}
 
-	var outErr error
-	for _, sh := range shs {
-		if err := cs.deleteShardFile(ctx, sh); err != nil {
-			if !os.IsNotExist(err) {
-				return err
+		var outErr error
+		for _, sh := range subs {
+			if err := cs.deleteShardFile(ctx, sh); err != nil {
+				if !os.IsNotExist(err) {
+					return err
+				}
+				outErr = err
 			}
-			outErr = err
 		}
+
+		return outErr
 	}
 
-	return outErr
+	chunkSize := 100
+	for i := 0; i < len(shs); i += chunkSize {
+		sl := shs[i:]
+		if len(sl) > chunkSize {
+			sl = sl[:chunkSize]
+		}
+
+		if err := deleteSlice(ctx, sl); err != nil {
+			return err
+		}
+	}
+
+	return nil
 }
 
 type shardStat struct {
@@ -1135,7 +1151,7 @@ func (cs *CarStore) CompactUserShards(ctx context.Context, user models.Uid) erro
 	span.SetAttributes(attribute.Int64("user", int64(user)))
 
 	var shards []CarShard
-	if err := cs.meta.Find(&shards, "usr = ?", user).Error; err != nil {
+	if err := cs.meta.WithContext(ctx).Find(&shards, "usr = ?", user).Error; err != nil {
 		return err
 	}
 
@@ -1150,12 +1166,12 @@ func (cs *CarStore) CompactUserShards(ctx context.Context, user models.Uid) erro
 	}
 
 	var brefs []blockRef
-	if err := cs.meta.Debug().Raw(`select * from block_refs where shard in (?)`, shardIds).Scan(&brefs).Error; err != nil {
+	if err := cs.meta.WithContext(ctx).Raw(`select * from block_refs where shard in (?)`, shardIds).Scan(&brefs).Error; err != nil {
 		return err
 	}
 
 	var staleRefs []staleRef
-	if err := cs.meta.Debug().Find(&staleRefs, "usr = ?", user).Error; err != nil {
+	if err := cs.meta.WithContext(ctx).Find(&staleRefs, "usr = ?", user).Error; err != nil {
 		return err
 	}
 
@@ -1244,6 +1260,13 @@ func (cs *CarStore) CompactUserShards(ctx context.Context, user models.Uid) erro
 	// now we need to delete the staleRefs we successfully cleaned up
 	// we can delete a staleRef if all the shards that have blockRefs with matching stale refs were processed
 
+	return cs.deleteStaleRefs(ctx, brefs, staleRefs, removedShards)
+}
+
+func (cs *CarStore) deleteStaleRefs(ctx context.Context, brefs []blockRef, staleRefs []staleRef, removedShards map[uint]bool) error {
+	ctx, span := otel.Tracer("carstore").Start(ctx, "deleteStaleRefs")
+	defer span.End()
+
 	brByCid := make(map[cid.Cid][]blockRef)
 	for _, br := range brefs {
 		brByCid[br.Cid.CID] = append(brByCid[br.Cid.CID], br)
@@ -1265,8 +1288,16 @@ func (cs *CarStore) CompactUserShards(ctx context.Context, user models.Uid) erro
 		}
 	}
 
-	if err := cs.meta.Delete(&staleRef{}, "id in (?)", staleToDelete).Error; err != nil {
-		return err
+	chunkSize := 100
+	for i := 0; i < len(staleToDelete); i += chunkSize {
+		sl := staleToDelete[i:]
+		if len(sl) > chunkSize {
+			sl = sl[:chunkSize]
+		}
+
+		if err := cs.meta.Delete(&staleRef{}, "id in (?)", sl).Error; err != nil {
+			return err
+		}
 	}
 
 	return nil