diff --git a/scanner/phase_1_folders.go b/scanner/phase_1_folders.go
index 3d04d525d..fb78e81a4 100644
--- a/scanner/phase_1_folders.go
+++ b/scanner/phase_1_folders.go
@@ -27,31 +27,14 @@ import (
 )
 
 func createPhaseFolders(ctx context.Context, state *scanState, ds model.DataStore, cw artwork.CacheWarmer) *phaseFolders {
+	// At this point, all libraries in state.libraries have been initialized
+	// (LastScanStartedAt has been set by prepareLibrariesForScan in scanner.go)
 	var jobs []*scanJob
-	var updatedLibs []model.Library
-	for _, lib := range state.libraries {
-		if lib.LastScanStartedAt.IsZero() {
-			err := ds.Library(ctx).ScanBegin(lib.ID, state.fullScan)
-			if err != nil {
-				log.Error(ctx, "Scanner: Error updating last scan started at", "lib", lib.Name, err)
-				state.sendWarning(err.Error())
-				continue
-			}
-			// Reload library to get updated state
-			l, err := ds.Library(ctx).Get(lib.ID)
-			if err != nil {
-				log.Error(ctx, "Scanner: Error reloading library", "lib", lib.Name, err)
-				state.sendWarning(err.Error())
-				continue
-			}
-			lib = *l
-		} else {
-			log.Debug(ctx, "Scanner: Resuming previous scan", "lib", lib.Name, "lastScanStartedAt", lib.LastScanStartedAt, "fullScan", lib.FullScanInProgress)
-		}
 
+	for _, lib := range state.libraries {
 		// Get target folders for this library if selective scan
 		var targetFolders []string
-		if state.targets != nil {
+		if state.isSelectiveScan() {
 			targetFolders = state.targets[lib.ID]
 		}
 
@@ -62,12 +45,8 @@ func createPhaseFolders(ctx context.Context, state *scanState, ds model.DataStor
 			continue
 		}
 		jobs = append(jobs, job)
-		updatedLibs = append(updatedLibs, lib)
 	}
 
-	// Update the state with the libraries that have been processed and have their scan timestamps set
-	state.libraries = updatedLibs
-
 	return &phaseFolders{jobs: jobs, ctx: ctx, ds: ds, state: state}
 }
 
diff --git a/scanner/phase_2_missing_tracks.go b/scanner/phase_2_missing_tracks.go
index a6c0e261e..de93ed6ee 100644
--- a/scanner/phase_2_missing_tracks.go
+++ b/scanner/phase_2_missing_tracks.go
@@ -69,9 +69,6 @@ func (p *phaseMissingTracks) produce(put func(tracks *missingTracks)) error {
 		}
 	}
 	for _, lib := range p.state.libraries {
-		if lib.LastScanStartedAt.IsZero() {
-			continue
-		}
 		log.Debug(p.ctx, "Scanner: Checking missing tracks", "libraryId", lib.ID, "libraryName", lib.Name)
 		cursor, err := p.ds.MediaFile(p.ctx).GetMissingAndMatching(lib.ID)
 		if err != nil {
diff --git a/scanner/scanner.go b/scanner/scanner.go
index c0bf98c26..539e52933 100644
--- a/scanner/scanner.go
+++ b/scanner/scanner.go
@@ -123,6 +123,14 @@ func (s *scannerImpl) scanFolders(ctx context.Context, fullScan bool, targets []
 		}
 	}
 
+	// Prepare libraries for scanning (initialize LastScanStartedAt if needed)
+	err = s.prepareLibrariesForScan(ctx, &state)
+	if err != nil {
+		log.Error(ctx, "Scanner: Error preparing libraries for scan", err)
+		state.sendError(err)
+		return
+	}
+
 	err = run.Sequentially(
 		// Phase 1: Scan all libraries and import new/updated files
 		runPhase[*folderEntry](ctx, 1, createPhaseFolders(ctx, &state, s.ds, s.cw)),
@@ -173,6 +181,48 @@ func (s *scannerImpl) scanFolders(ctx context.Context, fullScan bool, targets []
 	}
 }
 
+// prepareLibrariesForScan initializes the scan for all libraries in the state.
+// It calls ScanBegin for libraries that haven't started scanning yet (LastScanStartedAt is zero),
+// reloads them to get the updated state, and filters out any libraries that fail to initialize.
+func (s *scannerImpl) prepareLibrariesForScan(ctx context.Context, state *scanState) error {
+	var successfulLibs []model.Library
+
+	for _, lib := range state.libraries {
+		if lib.LastScanStartedAt.IsZero() {
+			// This is a new scan - mark it as started
+			err := s.ds.Library(ctx).ScanBegin(lib.ID, state.fullScan)
+			if err != nil {
+				log.Error(ctx, "Scanner: Error marking scan start", "lib", lib.Name, err)
+				state.sendWarning(err.Error())
+				continue
+			}
+
+			// Reload library to get updated state (timestamps, etc.)
+			reloadedLib, err := s.ds.Library(ctx).Get(lib.ID)
+			if err != nil {
+				log.Error(ctx, "Scanner: Error reloading library", "lib", lib.Name, err)
+				state.sendWarning(err.Error())
+				continue
+			}
+			lib = *reloadedLib
+		} else {
+			// This is a resumed scan
+			log.Debug(ctx, "Scanner: Resuming previous scan", "lib", lib.Name,
+				"lastScanStartedAt", lib.LastScanStartedAt, "fullScan", lib.FullScanInProgress)
+		}
+
+		successfulLibs = append(successfulLibs, lib)
+	}
+
+	if len(successfulLibs) == 0 {
+		return fmt.Errorf("no libraries available for scanning")
+	}
+
+	// Update state with only successfully initialized libraries
+	state.libraries = successfulLibs
+	return nil
+}
+
 func (s *scannerImpl) runGC(ctx context.Context, state *scanState) func() error {
 	return func() error {
 		state.sendProgress(&ProgressInfo{ForceUpdate: true})