diff --git a/sea-orm-cli/src/commands/generate.rs b/sea-orm-cli/src/commands/generate.rs
index 36fcd8441..b2a28ec55 100644
--- a/sea-orm-cli/src/commands/generate.rs
+++ b/sea-orm-cli/src/commands/generate.rs
@@ -137,7 +137,7 @@ pub async fn run_generate_command(
                         sqlx_connect::<Sqlite>(max_connections, url.as_str(), None).await?;
                     println!("Discovering schema ...");
                     let schema_discovery = SchemaDiscovery::new(connection);
-                    let schema = schema_discovery.discover().await?.collect_unique_indexes();
+                    let schema = schema_discovery.discover().await?.merge_indexes_into_table();
                     let table_stmts = schema
                         .tables
                         .into_iter()