diff --git a/openmetadata-service/src/main/java/org/openmetadata/service/util/TablesInitializer.java b/openmetadata-service/src/main/java/org/openmetadata/service/util/TablesInitializer.java
index 3c438e224e1..065e900ec8e 100644
--- a/openmetadata-service/src/main/java/org/openmetadata/service/util/TablesInitializer.java
+++ b/openmetadata-service/src/main/java/org/openmetadata/service/util/TablesInitializer.java
@@ -274,6 +274,8 @@ public final class TablesInitializer {
           }
         }
         flyway.migrate();
+        validateAndRunSystemDataMigrations(
+            jdbi, ConnectionType.from(config.getDataSourceFactory().getDriverClass()), ignoreServerFileChecksum);
         break;
       case MIGRATE:
         flyway.migrate();