diff --git a/storage/localstore/localstore_test.go b/storage/localstore/localstore_test.go
index ace0a10dcb..41d757506e 100644
--- a/storage/localstore/localstore_test.go
+++ b/storage/localstore/localstore_test.go
@@ -613,6 +613,6 @@ func TestDBDebugIndexes(t *testing.T) {
 	}
 
 	// assert that there's a pin and gc exclude entry now
-	testIndexCounts(t, 1, 1, 1, 1, 1, 1, 1, indexCounts)
+	testIndexCounts(t, 1, 1, 0, 1, 1, 1, 1, indexCounts)
 
 }
diff --git a/storage/localstore/mode_get.go b/storage/localstore/mode_get.go
index 0ad8825a19..d86d60b77d 100644
--- a/storage/localstore/mode_get.go
+++ b/storage/localstore/mode_get.go
@@ -154,7 +154,16 @@ func (db *DB) updateGC(item shed.Item) (err error) {
 	// update retrieve access index
 	db.retrievalAccessIndex.PutInBatch(batch, item)
 	// add new entry to gc index
-	db.gcIndex.PutInBatch(batch, item)
+	ok, err := db.pinIndex.Has(item)
+	if err != nil {
+		return err
+	}
+	if !ok {
+		err = db.gcIndex.PutInBatch(batch, item)
+		if err != nil {
+			return err
+		}
+	}
 
 	return db.shed.WriteBatch(batch)
 }
diff --git a/storage/localstore/mode_put.go b/storage/localstore/mode_put.go
index 8de4cc0f7f..dc48436621 100644
--- a/storage/localstore/mode_put.go
+++ b/storage/localstore/mode_put.go
@@ -317,8 +317,17 @@ func (db *DB) setGC(batch *leveldb.Batch, item shed.Item) (gcSizeChange int64, e
 	item.AccessTimestamp = now()
 	db.retrievalAccessIndex.PutInBatch(batch, item)
 
-	db.gcIndex.PutInBatch(batch, item)
-	gcSizeChange++
+	ok, err := db.pinIndex.Has(item)
+	if err != nil {
+		return 0, err
+	}
+	if !ok {
+		err = db.gcIndex.PutInBatch(batch, item)
+		if err != nil {
+			return 0, err
+		}
+		gcSizeChange++
+	}
 
 	return gcSizeChange, nil
 }
diff --git a/storage/localstore/mode_set.go b/storage/localstore/mode_set.go
index 319ec1bf87..7703532fdc 100644
--- a/storage/localstore/mode_set.go
+++ b/storage/localstore/mode_set.go
@@ -171,8 +171,18 @@ func (db *DB) setAccess(batch *leveldb.Batch, binIDs map[uint8]uint64, addr chun
 	item.AccessTimestamp = now()
 	db.retrievalAccessIndex.PutInBatch(batch, item)
 	db.pullIndex.PutInBatch(batch, item)
-	db.gcIndex.PutInBatch(batch, item)
-	gcSizeChange++
+
+	ok, err := db.pinIndex.Has(item)
+	if err != nil {
+		return 0, err
+	}
+	if !ok {
+		err = db.gcIndex.PutInBatch(batch, item)
+		if err != nil {
+			return 0, err
+		}
+		gcSizeChange++
+	}
 
 	return gcSizeChange, nil
 }
@@ -296,7 +306,10 @@ func (db *DB) setSync(batch *leveldb.Batch, addr chunk.Address, mode chunk.ModeS
 		return 0, err
 	}
 	if !ok {
-		db.gcIndex.PutInBatch(batch, item)
+		err = db.gcIndex.PutInBatch(batch, item)
+		if err != nil {
+			return 0, err
+		}
 		gcSizeChange++
 	}