diff --git a/cmd/cleanup-index/main.go b/cmd/cleanup-index/main.go
index 4a78e0522..143aeafde 100644
--- a/cmd/cleanup-index/main.go
+++ b/cmd/cleanup-index/main.go
@@ -63,8 +63,8 @@ var (
 	redisEnableTLS          = flag.Bool("redis-enable-tls", false, "Enable TLS for Redis client")
 	redisInsecureSkipVerify = flag.Bool("redis-insecure-skip-verify", false, "Whether to skip TLS verification for Redis client or not")
 	mysqlDSN                = flag.String("mysql-dsn", "", "MySQL Data Source Name")
-	versionFlag             = flag.Bool("version", false, "Print the current version of Backfill MySQL")
-	dryRun                  = flag.Bool("dry-run", false, "Dry run - don't actually insert into MySQL")
+	versionFlag             = flag.Bool("version", false, "Print the current version of cleanup-index")
+	dryRun                  = flag.Bool("dry-run", false, "Dry run - don't actually delete from Redis")
 )
 
 func main() {
@@ -97,13 +97,9 @@ func main() {
 
 	ctx, _ := signal.NotifyContext(context.Background(), os.Interrupt, syscall.SIGTERM)
 
-	keys, err := getKeysToDelete(ctx, mysqlClient)
+	err = batchQueryAndDelete(ctx, mysqlClient, redisClient)
 	if err != nil {
-		log.Fatalf("getting keys from mysql: %v", err)
-	}
-	err = removeFromRedis(ctx, redisClient, keys)
-	if err != nil {
-		log.Fatalf("deleting keys from redis: %v", err)
+		log.Fatal(err)
 	}
 }
 
@@ -136,16 +132,42 @@ func getMySQLClient() (*sqlx.DB, error) {
 	return dbClient, nil
 }
 
-// getKeysToDelete looks up entries in the EntryIndex table in MySQL.
-func getKeysToDelete(ctx context.Context, dbClient *sqlx.DB) ([]string, error) {
-	keys := []string{}
-	err := dbClient.SelectContext(ctx, &keys, mysqlSelectStmt)
-	return keys, err
+// batchQueryAndDelete looks up entries in the EntryIndex table in MySQL and removes them from Redis.
+// The SQL query is processed in batches because the entire data set is too large to store in memory at once.
+func batchQueryAndDelete(ctx context.Context, dbClient *sqlx.DB, redisClient *redis.Client) error {
+	const batchSize = 10000
+	keys := [batchSize]string{}
+	rows, err := dbClient.QueryContext(ctx, mysqlSelectStmt)
+	if err != nil {
+		return err
+	}
+	defer rows.Close()
+	index := 0
+	batchIndex := 1
+	for rows.Next() {
+		if err := rows.Scan(&keys[index]); err != nil {
+			return err
+		}
+		index++
+		if index == batchSize {
+			if err := removeFromRedis(ctx, redisClient, keys[:], batchIndex); err != nil {
+				return err
+			}
+			index = 0
+			batchIndex++
+		}
+	}
+	if index != 0 {
+		if err := removeFromRedis(ctx, redisClient, keys[:index], batchIndex); err != nil {
+			return err
+		}
+	}
+	return nil
 }
 
 // removeFromRedis delete the given keys from Redis.
-func removeFromRedis(ctx context.Context, redisClient *redis.Client, keys []string) error {
-	fmt.Printf("attempting to remove %d keys from redis\n", len(keys))
+func removeFromRedis(ctx context.Context, redisClient *redis.Client, keys []string, batchIndex int) error {
+	fmt.Printf("attempting to remove %d keys from redis (batch %d)\n", len(keys), batchIndex)
 	if *dryRun {
 		return nil
 	}