diff --git a/src/server/api/auth.py b/src/server/api/auth.py
index 34d8953..12a67d3 100644
--- a/src/server/api/auth.py
+++ b/src/server/api/auth.py
@@ -51,10 +51,10 @@ async def setup_auth(req: SetupRequest):
         except Exception:
             # If config doesn't exist, create default
             from src.server.models.config import (
-                SchedulerConfig,
-                LoggingConfig,
                 BackupConfig,
+                LoggingConfig,
                 NFOConfig,
+                SchedulerConfig,
             )
             config = AppConfig()
         
@@ -122,6 +122,10 @@ async def setup_auth(req: SetupRequest):
             try:
                 import structlog
 
+                from src.server.database.connection import get_db_session
+                from src.server.database.system_settings_service import (
+                    SystemSettingsService,
+                )
                 from src.server.services.anime_service import (
                     sync_series_from_data_files,
                 )
@@ -133,6 +137,19 @@ async def setup_auth(req: SetupRequest):
                     "Setup complete: synced series from data files",
                     count=sync_count
                 )
+                
+                # Mark initial scan as completed
+                try:
+                    async with get_db_session() as db:
+                        await SystemSettingsService.mark_initial_scan_completed(
+                            db
+                        )
+                    logger.info("Marked initial scan as completed")
+                except Exception as mark_error:
+                    logger.warning(
+                        "Failed to mark initial scan as completed",
+                        error=str(mark_error)
+                    )
             except Exception as e:
                 # Log but don't fail setup if sync fails
                 import structlog