diff --git a/src/server/services/initialization_service.py b/src/server/services/initialization_service.py
index 5bb1fd8..840e9c7 100644
--- a/src/server/services/initialization_service.py
+++ b/src/server/services/initialization_service.py
@@ -215,6 +215,20 @@ async def _sync_anime_folders(progress_service=None) -> int:
     """
     logger.info("Performing initial anime folder scan...")
     
+    # Check if anime directory exists before attempting sync
+    if not settings.anime_directory or not os.path.isdir(settings.anime_directory):
+        logger.info(
+            "Anime directory not configured or does not exist, skipping data file sync"
+        )
+        if progress_service:
+            await progress_service.update_progress(
+                progress_id="series_sync",
+                current=100,
+                message="No anime directory configured, skipping data file sync",
+                metadata={"step_id": "series_sync"}
+            )
+        return 0
+    
     if progress_service:
         await progress_service.update_progress(
             progress_id="series_sync",
diff --git a/src/server/services/scheduler/scheduler_service.py b/src/server/services/scheduler/scheduler_service.py
index 241ed33..0d03e87 100644
--- a/src/server/services/scheduler/scheduler_service.py
+++ b/src/server/services/scheduler/scheduler_service.py
@@ -323,8 +323,18 @@ class SchedulerService:
             async with get_db_session() as db:
                 settings = await SystemSettingsService.get_or_create(db)
                 last_scan = settings.last_scan_timestamp
+                initial_scan_done = settings.initial_scan_completed
 
             if last_scan is None:
+                # No previous scan recorded
+                if not initial_scan_done:
+                    # Initial setup not yet completed - skip rescan
+                    # The setup flow will trigger rescan when ready
+                    logger.info(
+                        "No previous scan recorded and initial setup not yet "
+                        "completed — skipping immediate rescan"
+                    )
+                    return
                 # Never scanned before — trigger immediately
                 logger.info("No previous scan recorded — triggering immediate rescan")
                 await self._perform_rescan()
diff --git a/tests/unit/test_initialization_service.py b/tests/unit/test_initialization_service.py
index 7276c91..6194adb 100644
--- a/tests/unit/test_initialization_service.py
+++ b/tests/unit/test_initialization_service.py
@@ -160,8 +160,11 @@ class TestSyncAnimeFolders:
     @pytest.mark.asyncio
     async def test_sync_anime_folders_without_progress(self):
         """Test syncing anime folders without progress service."""
-        with patch('src.server.services.initialization_service.sync_legacy_series_to_db', 
+        with patch('src.server.services.initialization_service.settings') as mock_settings, \
+             patch('src.server.services.initialization_service.os.path.isdir', return_value=True), \
+             patch('src.server.services.initialization_service.sync_legacy_series_to_db', 
                    new_callable=AsyncMock, return_value=42) as mock_sync:
+            mock_settings.anime_directory = "/path/to/anime"
             result = await _sync_anime_folders()
         
         assert result == 42
@@ -172,8 +175,11 @@ class TestSyncAnimeFolders:
         """Test syncing anime folders with progress updates."""
         mock_progress = AsyncMock()
         
-        with patch('src.server.services.initialization_service.sync_legacy_series_to_db', 
+        with patch('src.server.services.initialization_service.settings') as mock_settings, \
+             patch('src.server.services.initialization_service.os.path.isdir', return_value=True), \
+             patch('src.server.services.initialization_service.sync_legacy_series_to_db', 
                    new_callable=AsyncMock, return_value=10) as mock_sync:
+            mock_settings.anime_directory = "/path/to/anime"
             result = await _sync_anime_folders(progress_service=mock_progress)
         
         assert result == 10