diff --git a/internal/storage/qdrant.go b/internal/storage/qdrant.go
index 6d77f9b..59c9d63 100644
--- a/internal/storage/qdrant.go
+++ b/internal/storage/qdrant.go
@@ -3,6 +3,7 @@ package storage
 import (
 	"context"
 	"fmt"
+	"strings"
 
 	"github.com/qdrant/go-client/qdrant"
 )
@@ -515,6 +516,53 @@ func (c *QdrantClient) DeleteByFilter(ctx context.Context, key, value string) er
 	return nil
 }
 
+// DeleteByPrefix deletes all vectors where the payload field `key` starts with `prefix`.
+// Uses Scroll to find matching points (client-side prefix filter) then batch deletes them.
+// Returns the number of deleted points.
+func (c *QdrantClient) DeleteByPrefix(ctx context.Context, key, prefix string) (int, error) {
+	// Single-pass scroll: request all points with only the target payload field.
+	// Workspace collections typically have <10k points, so a single pass is fine.
+	// If pagination is needed in the future, the Scroll Offset field can be used.
+	results, err := c.client.Scroll(ctx, &qdrant.ScrollPoints{
+		CollectionName: c.config.Collection,
+		Limit:          qdrant.PtrOf(uint32(50000)),
+		WithPayload:    qdrant.NewWithPayloadInclude(key),
+	})
+	if err != nil {
+		return 0, fmt.Errorf("scroll for prefix %q failed: %w", prefix, err)
+	}
+
+	var allMatchingIDs []*qdrant.PointId
+	for _, point := range results {
+		if val, ok := point.Payload[key]; ok {
+			if strings.HasPrefix(val.GetStringValue(), prefix) {
+				allMatchingIDs = append(allMatchingIDs, point.Id)
+			}
+		}
+	}
+
+	if len(allMatchingIDs) == 0 {
+		return 0, nil
+	}
+
+	// Batch delete all matching point IDs
+	_, err = c.client.Delete(ctx, &qdrant.DeletePoints{
+		CollectionName: c.config.Collection,
+		Points: &qdrant.PointsSelector{
+			PointsSelectorOneOf: &qdrant.PointsSelector_Points{
+				Points: &qdrant.PointsIdsList{
+					Ids: allMatchingIDs,
+				},
+			},
+		},
+	})
+	if err != nil {
+		return 0, fmt.Errorf("batch delete of %d points by prefix %q failed: %w", len(allMatchingIDs), prefix, err)
+	}
+
+	return len(allMatchingIDs), nil
+}
+
 // Close closes the Qdrant client connection
 func (c *QdrantClient) Close() error {
 	if c.client != nil {
diff --git a/internal/workspace/manager.go b/internal/workspace/manager.go
index f6acb64..9058cbc 100644
--- a/internal/workspace/manager.go
+++ b/internal/workspace/manager.go
@@ -634,13 +634,43 @@ func (m *Manager) IndexLanguage(ctx context.Context, info *Info, language string
 	}
 
 	// Check for deleted files (both code and docs)
-	// We scan the state and check if files still exist in current scan
-	// But scan only has current files.
-	// Better: iterate state.Files and check if they exist on disk.
-	state.mu.RLock()
-	for path := range state.Files {
-		if _, err := os.Stat(path); os.IsNotExist(err) {
-			// It's deleted. Determine if it was code or doc based on extension
+	// Use directory-aware cleanup: detect the highest deleted directory and
+	// bulk-remove all vectors under it rather than deleting one by one.
+	staleFiles := CollectStaleFiles(state)
+
+	if len(staleFiles) > 0 {
+		dirPrefixes, individualStale := GroupByDeletedRoot(staleFiles, info.Root)
+
+		// --- Bulk delete for entire deleted directories ---
+		for prefix, files := range dirPrefixes {
+			log.Printf("🔍 Detected deleted directory: %s (%d tracked files)", prefix, len(files))
+
+			deleted, delErr := collectionClient.DeleteByPrefix(ctx, "file", prefix)
+			if delErr != nil {
+				log.Printf("⚠️  Prefix delete failed for %s: %v — falling back to per-file delete", prefix, delErr)
+				// Fallback: delete individually
+				for _, path := range files {
+					if err := ltm.DeleteByMetadata(ctx, "file", path); err != nil {
+						log.Printf("⚠️  Failed to delete chunks for %s: %v", path, err)
+					}
+				}
+			} else if deleted > 0 {
+				log.Printf("🧹 Bulk-deleted %d vectors under %s", deleted, prefix)
+			}
+
+			// Also remove any other state entries that match this prefix
+			// (files we haven't seen in staleFiles because they weren't in the iteration)
+			state.mu.Lock()
+			for path := range state.Files {
+				if strings.HasPrefix(path, prefix) {
+					delete(state.Files, path)
+				}
+			}
+			state.mu.Unlock()
+		}
+
+		// --- Individual file deletions (parent dir still exists) ---
+		for _, path := range individualStale {
 			ext := strings.ToLower(filepath.Ext(path))
 			if ext == ".md" {
 				docsToDelete = append(docsToDelete, path)
@@ -649,7 +679,6 @@ func (m *Manager) IndexLanguage(ctx context.Context, info *Info, language string
 			}
 		}
 	}
-	state.mu.RUnlock()
 
 	// Process deletions (Code)
 	if len(filesToDelete) > 0 {
diff --git a/internal/workspace/stale.go b/internal/workspace/stale.go
new file mode 100644
index 0000000..c4a3177
--- /dev/null
+++ b/internal/workspace/stale.go
@@ -0,0 +1,86 @@
+package workspace
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+)
+
+// FindDeletedRoot walks up from filePath to find the highest deleted directory.
+// If only the file itself is missing but its parent directory exists, returns filePath.
+// If a parent directory is also missing, walks further up to find the topmost deleted ancestor
+// below workspaceRoot.
+//
+// Example:
+//
+//	Given: filePath="/project/tmp/vendor/src/foo.php", workspaceRoot="/project"
+//	If /project/tmp/ was deleted entirely:
+//	  Returns "/project/tmp" (the highest missing ancestor)
+func FindDeletedRoot(filePath, workspaceRoot string) string {
+	highestDeleted := filePath
+	dir := filepath.Dir(filePath)
+	wsClean := filepath.Clean(workspaceRoot)
+
+	for {
+		dirClean := filepath.Clean(dir)
+		// Stop if we've reached the workspace root or filesystem root
+		if dirClean == wsClean || dirClean == "/" || dirClean == "." {
+			break
+		}
+
+		if _, err := os.Stat(dir); os.IsNotExist(err) {
+			// This directory is also deleted — record it and keep going up
+			highestDeleted = dir
+			dir = filepath.Dir(dir)
+			continue
+		}
+		// Directory exists — stop here
+		break
+	}
+
+	return filepath.Clean(highestDeleted)
+}
+
+// IsDirectoryDeletion returns true if the deleted root is a directory path
+// (i.e., a parent directory was deleted, not just the individual file).
+func IsDirectoryDeletion(deletedRoot, originalFile string) bool {
+	return filepath.Clean(deletedRoot) != filepath.Clean(originalFile)
+}
+
+// CollectStaleFiles iterates WorkspaceState.Files and returns paths
+// that no longer exist on disk.
+func CollectStaleFiles(state *WorkspaceState) []string {
+	state.mu.RLock()
+	defer state.mu.RUnlock()
+
+	var stale []string
+	for path := range state.Files {
+		if _, err := os.Stat(path); os.IsNotExist(err) {
+			stale = append(stale, path)
+		}
+	}
+	return stale
+}
+
+// GroupByDeletedRoot groups stale file paths by their highest deleted ancestor directory.
+// Returns two maps:
+//   - dirPrefixes: map[prefix][]filePath — files under a deleted directory
+//   - individualFiles: files whose parent directory still exists
+func GroupByDeletedRoot(staleFiles []string, workspaceRoot string) (dirPrefixes map[string][]string, individualFiles []string) {
+	dirPrefixes = make(map[string][]string)
+
+	for _, f := range staleFiles {
+		root := FindDeletedRoot(f, workspaceRoot)
+		if IsDirectoryDeletion(root, f) {
+			prefix := root
+			if !strings.HasSuffix(prefix, string(os.PathSeparator)) {
+				prefix += string(os.PathSeparator)
+			}
+			dirPrefixes[prefix] = append(dirPrefixes[prefix], f)
+		} else {
+			individualFiles = append(individualFiles, f)
+		}
+	}
+
+	return dirPrefixes, individualFiles
+}
diff --git a/internal/workspace/stale_test.go b/internal/workspace/stale_test.go
new file mode 100644
index 0000000..4a49ba7
--- /dev/null
+++ b/internal/workspace/stale_test.go
@@ -0,0 +1,151 @@
+package workspace
+
+import (
+	"os"
+	"path/filepath"
+	"sort"
+	"testing"
+)
+
+func TestFindDeletedRoot_FileOnlyDeleted(t *testing.T) {
+	// Setup: create workspace/dir/subdir/ but NOT the file inside it
+	wsRoot := t.TempDir()
+	subdir := filepath.Join(wsRoot, "src", "pkg")
+	if err := os.MkdirAll(subdir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	// File that doesn't exist, but parent directory does
+	missingFile := filepath.Join(subdir, "deleted.go")
+
+	result := FindDeletedRoot(missingFile, wsRoot)
+	if result != missingFile {
+		t.Errorf("expected %q, got %q — when only the file is missing, should return the file path itself", missingFile, result)
+	}
+}
+
+func TestFindDeletedRoot_DirectoryDeleted(t *testing.T) {
+	// Setup: workspace root exists, but "tmp" directory does NOT
+	wsRoot := t.TempDir()
+
+	// Neither tmp/ nor its children exist
+	missingFile := filepath.Join(wsRoot, "tmp", "vendor", "src", "foo.php")
+
+	result := FindDeletedRoot(missingFile, wsRoot)
+	expected := filepath.Join(wsRoot, "tmp")
+	if result != expected {
+		t.Errorf("expected %q, got %q — should return the highest deleted directory", expected, result)
+	}
+}
+
+func TestFindDeletedRoot_IntermediateDirectoryDeleted(t *testing.T) {
+	// Setup: workspace/src/ exists, but workspace/src/old/ does NOT
+	wsRoot := t.TempDir()
+	srcDir := filepath.Join(wsRoot, "src")
+	if err := os.MkdirAll(srcDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	// src/ exists, but src/old/ and deeper don't
+	missingFile := filepath.Join(wsRoot, "src", "old", "legacy", "file.go")
+
+	result := FindDeletedRoot(missingFile, wsRoot)
+	expected := filepath.Join(wsRoot, "src", "old")
+	if result != expected {
+		t.Errorf("expected %q, got %q — should return the highest deleted directory below existing parent", expected, result)
+	}
+}
+
+func TestFindDeletedRoot_WorkspaceRootBoundary(t *testing.T) {
+	// Ensure we never go above workspace root
+	wsRoot := t.TempDir()
+
+	// Everything under workspace root is deleted
+	missingFile := filepath.Join(wsRoot, "a", "b", "c", "d.txt")
+
+	result := FindDeletedRoot(missingFile, wsRoot)
+	expected := filepath.Join(wsRoot, "a")
+	if result != expected {
+		t.Errorf("expected %q, got %q — should stop at direct child of workspace root", expected, result)
+	}
+}
+
+func TestIsDirectoryDeletion(t *testing.T) {
+	tests := []struct {
+		deletedRoot  string
+		originalFile string
+		expected     bool
+	}{
+		{"/project/tmp", "/project/tmp/foo.php", true},
+		{"/project/foo.go", "/project/foo.go", false},
+		{"/project/src/old", "/project/src/old/deep/file.go", true},
+	}
+
+	for _, tt := range tests {
+		result := IsDirectoryDeletion(tt.deletedRoot, tt.originalFile)
+		if result != tt.expected {
+			t.Errorf("IsDirectoryDeletion(%q, %q) = %v, want %v",
+				tt.deletedRoot, tt.originalFile, result, tt.expected)
+		}
+	}
+}
+
+func TestGroupByDeletedRoot(t *testing.T) {
+	wsRoot := t.TempDir()
+
+	// Create src/ (exists) but not tmp/ (deleted)
+	srcDir := filepath.Join(wsRoot, "src")
+	if err := os.MkdirAll(srcDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	staleFiles := []string{
+		filepath.Join(wsRoot, "tmp", "a", "file1.go"),
+		filepath.Join(wsRoot, "tmp", "b", "file2.go"),
+		filepath.Join(wsRoot, "src", "deleted.go"), // parent exists, only file missing
+	}
+
+	dirPrefixes, individualFiles := GroupByDeletedRoot(staleFiles, wsRoot)
+
+	// tmp/ is the deleted root for both tmp files
+	expectedPrefix := filepath.Join(wsRoot, "tmp") + string(os.PathSeparator)
+	if _, ok := dirPrefixes[expectedPrefix]; !ok {
+		t.Errorf("expected prefix %q in dirPrefixes, got: %v", expectedPrefix, dirPrefixes)
+	}
+
+	if len(dirPrefixes[expectedPrefix]) != 2 {
+		t.Errorf("expected 2 files under prefix %q, got %d", expectedPrefix, len(dirPrefixes[expectedPrefix]))
+	}
+
+	sort.Strings(individualFiles)
+	expectedIndividual := filepath.Join(wsRoot, "src", "deleted.go")
+	if len(individualFiles) != 1 || individualFiles[0] != expectedIndividual {
+		t.Errorf("expected individualFiles = [%q], got %v", expectedIndividual, individualFiles)
+	}
+}
+
+func TestCollectStaleFiles(t *testing.T) {
+	wsRoot := t.TempDir()
+
+	// Create a real file
+	existingFile := filepath.Join(wsRoot, "exists.go")
+	if err := os.WriteFile(existingFile, []byte("package main"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create state with both existing and non-existing files
+	state := NewWorkspaceState()
+
+	realInfo, _ := os.Stat(existingFile)
+	state.UpdateFile(existingFile, realInfo)
+	state.Files[filepath.Join(wsRoot, "deleted.go")] = FileState{}
+
+	stale := CollectStaleFiles(state)
+
+	if len(stale) != 1 {
+		t.Fatalf("expected 1 stale file, got %d: %v", len(stale), stale)
+	}
+	if stale[0] != filepath.Join(wsRoot, "deleted.go") {
+		t.Errorf("expected stale file %q, got %q", filepath.Join(wsRoot, "deleted.go"), stale[0])
+	}
+}