diff --git a/internal/storage/sqlite/counter_sync_test.go b/internal/storage/sqlite/counter_sync_test.go
new file mode 100644
index 00000000..2ddae6c9
--- /dev/null
+++ b/internal/storage/sqlite/counter_sync_test.go
@@ -0,0 +1,232 @@
+package sqlite
+
+import (
+	"context"
+	"fmt"
+	"testing"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// TestCounterSyncAfterDelete verifies that counters are synced after deletion (bd-49)
+func TestCounterSyncAfterDelete(t *testing.T) {
+	store, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Set the issue prefix to "bd" for this test
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
+	// Create issues bd-1 through bd-5
+	for i := 1; i <= 5; i++ {
+		issue := &types.Issue{
+			ID:        genID("bd", i),
+			Title:     "Test issue",
+			Priority:  2,
+			IssueType: types.TypeTask,
+			Status:    types.StatusOpen,
+		}
+		if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+			t.Fatalf("Failed to create issue: %v", err)
+		}
+	}
+
+	// Create one issue with auto-generated ID to initialize counter
+	autoIssue := &types.Issue{
+		Title:     "Auto issue",
+		Priority:  2,
+		IssueType: types.TypeTask,
+		Status:    types.StatusOpen,
+	}
+	if err := store.CreateIssue(ctx, autoIssue, "test"); err != nil {
+		t.Fatalf("Failed to create auto issue: %v", err)
+	}
+	if autoIssue.ID != "bd-6" {
+		t.Fatalf("Expected auto issue to be bd-6, got %s", autoIssue.ID)
+	}
+
+	// Verify counter is at 6
+	var counter int
+	err := store.db.QueryRow(`SELECT last_id FROM issue_counters WHERE prefix = 'bd'`).Scan(&counter)
+	if err != nil {
+		t.Fatalf("Failed to query counter: %v", err)
+	}
+	if counter != 6 {
+		t.Errorf("Expected counter at 6, got %d", counter)
+	}
+
+	// Delete bd-5 and bd-6
+	if err := store.DeleteIssue(ctx, "bd-5"); err != nil {
+		t.Fatalf("Failed to delete bd-5: %v", err)
+	}
+	if err := store.DeleteIssue(ctx, "bd-6"); err != nil {
+		t.Fatalf("Failed to delete bd-6: %v", err)
+	}
+
+	// Counter should now be synced to 4 (max remaining ID)
+	err = store.db.QueryRow(`SELECT last_id FROM issue_counters WHERE prefix = 'bd'`).Scan(&counter)
+	if err != nil {
+		t.Fatalf("Failed to query counter after delete: %v", err)
+	}
+	if counter != 4 {
+		t.Errorf("Expected counter at 4 after deletion, got %d", counter)
+	}
+
+	// Create new issue - should be bd-5 (not bd-7)
+	newIssue := &types.Issue{
+		Title:     "New issue after deletion",
+		Priority:  2,
+		IssueType: types.TypeTask,
+		Status:    types.StatusOpen,
+	}
+	if err := store.CreateIssue(ctx, newIssue, "test"); err != nil {
+		t.Fatalf("Failed to create new issue: %v", err)
+	}
+	if newIssue.ID != "bd-5" {
+		t.Errorf("Expected new issue to be bd-5, got %s", newIssue.ID)
+	}
+}
+
+// TestCounterSyncAfterBatchDelete verifies that counters are synced after batch deletion (bd-49)
+func TestCounterSyncAfterBatchDelete(t *testing.T) {
+	store, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Set the issue prefix to "bd" for this test
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
+	// Create issues bd-1 through bd-10
+	for i := 1; i <= 10; i++ {
+		issue := &types.Issue{
+			ID:        genID("bd", i),
+			Title:     "Test issue",
+			Priority:  2,
+			IssueType: types.TypeTask,
+			Status:    types.StatusOpen,
+		}
+		if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+			t.Fatalf("Failed to create issue: %v", err)
+		}
+	}
+
+	// Create one issue with auto-generated ID to initialize counter
+	autoIssue := &types.Issue{
+		Title:     "Auto issue",
+		Priority:  2,
+		IssueType: types.TypeTask,
+		Status:    types.StatusOpen,
+	}
+	if err := store.CreateIssue(ctx, autoIssue, "test"); err != nil {
+		t.Fatalf("Failed to create auto issue: %v", err)
+	}
+	if autoIssue.ID != "bd-11" {
+		t.Fatalf("Expected auto issue to be bd-11, got %s", autoIssue.ID)
+	}
+
+	// Verify counter is at 11
+	var counter int
+	err := store.db.QueryRow(`SELECT last_id FROM issue_counters WHERE prefix = 'bd'`).Scan(&counter)
+	if err != nil {
+		t.Fatalf("Failed to query counter: %v", err)
+	}
+	if counter != 11 {
+		t.Errorf("Expected counter at 11, got %d", counter)
+	}
+
+	// Batch delete bd-6 through bd-11
+	toDelete := []string{"bd-6", "bd-7", "bd-8", "bd-9", "bd-10", "bd-11"}
+	_, err = store.DeleteIssues(ctx, toDelete, false, false, false)
+	if err != nil {
+		t.Fatalf("Failed to batch delete: %v", err)
+	}
+
+	// Counter should now be synced to 5 (max remaining ID)
+	err = store.db.QueryRow(`SELECT last_id FROM issue_counters WHERE prefix = 'bd'`).Scan(&counter)
+	if err != nil {
+		t.Fatalf("Failed to query counter after batch delete: %v", err)
+	}
+	if counter != 5 {
+		t.Errorf("Expected counter at 5 after batch deletion, got %d", counter)
+	}
+
+	// Create new issue - should be bd-6 (not bd-11)
+	newIssue := &types.Issue{
+		Title:     "New issue after batch deletion",
+		Priority:  2,
+		IssueType: types.TypeTask,
+		Status:    types.StatusOpen,
+	}
+	if err := store.CreateIssue(ctx, newIssue, "test"); err != nil {
+		t.Fatalf("Failed to create new issue: %v", err)
+	}
+	if newIssue.ID != "bd-6" {
+		t.Errorf("Expected new issue to be bd-6, got %s", newIssue.ID)
+	}
+}
+
+// TestCounterSyncAfterDeleteAll verifies counter resets when all issues deleted (bd-49)
+func TestCounterSyncAfterDeleteAll(t *testing.T) {
+	store, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Set the issue prefix to "bd" for this test
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+
+	// Create issues bd-1 through bd-5
+	for i := 1; i <= 5; i++ {
+		issue := &types.Issue{
+			ID:        genID("bd", i),
+			Title:     "Test issue",
+			Priority:  2,
+			IssueType: types.TypeTask,
+			Status:    types.StatusOpen,
+		}
+		if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+			t.Fatalf("Failed to create issue: %v", err)
+		}
+	}
+
+	// Delete all issues
+	toDelete := []string{"bd-1", "bd-2", "bd-3", "bd-4", "bd-5"}
+	_, err := store.DeleteIssues(ctx, toDelete, false, false, false)
+	if err != nil {
+		t.Fatalf("Failed to delete all issues: %v", err)
+	}
+
+	// Counter should be deleted (no issues left with this prefix)
+	var counter int
+	err = store.db.QueryRow(`SELECT last_id FROM issue_counters WHERE prefix = 'bd'`).Scan(&counter)
+	if err == nil {
+		t.Errorf("Expected no counter row, but found counter at %d", counter)
+	}
+
+	// Create new issue - should be bd-1 (fresh start)
+	newIssue := &types.Issue{
+		Title:     "First issue after deleting all",
+		Priority:  2,
+		IssueType: types.TypeTask,
+		Status:    types.StatusOpen,
+	}
+	if err := store.CreateIssue(ctx, newIssue, "test"); err != nil {
+		t.Fatalf("Failed to create new issue: %v", err)
+	}
+	if newIssue.ID != "bd-1" {
+		t.Errorf("Expected new issue to be bd-1, got %s", newIssue.ID)
+	}
+}
+
+// genID is a helper to generate issue IDs in tests
+func genID(prefix string, num int) string {
+	return fmt.Sprintf("%s-%d", prefix, num)
+}
diff --git a/internal/storage/sqlite/sqlite.go b/internal/storage/sqlite/sqlite.go
index e48c8bdc..e02ef877 100644
--- a/internal/storage/sqlite/sqlite.go
+++ b/internal/storage/sqlite/sqlite.go
@@ -463,8 +463,24 @@ func (s *SQLiteStorage) getNextIDForPrefix(ctx context.Context, prefix string) (
 
 // SyncAllCounters synchronizes all ID counters based on existing issues in the database
 // This scans all issues and updates counters to prevent ID collisions with auto-generated IDs
+// Note: This unconditionally overwrites counter values, allowing them to decrease after deletions
 func (s *SQLiteStorage) SyncAllCounters(ctx context.Context) error {
+	// First, delete counters for prefixes that have no issues
 	_, err := s.db.ExecContext(ctx, `
+		DELETE FROM issue_counters
+		WHERE prefix NOT IN (
+			SELECT DISTINCT substr(id, 1, instr(id, '-') - 1)
+			FROM issues
+			WHERE instr(id, '-') > 0
+			  AND substr(id, instr(id, '-') + 1) GLOB '[0-9]*'
+		)
+	`)
+	if err != nil {
+		return fmt.Errorf("failed to delete orphaned counters: %w", err)
+	}
+
+	// Then, upsert counters for prefixes that have issues
+	_, err = s.db.ExecContext(ctx, `
 		INSERT INTO issue_counters (prefix, last_id)
 		SELECT
 			substr(id, 1, instr(id, '-') - 1) as prefix,
@@ -474,7 +490,7 @@ func (s *SQLiteStorage) SyncAllCounters(ctx context.Context) error {
 		  AND substr(id, instr(id, '-') + 1) GLOB '[0-9]*'
 		GROUP BY prefix
 		ON CONFLICT(prefix) DO UPDATE SET
-			last_id = MAX(last_id, excluded.last_id)
+			last_id = excluded.last_id
 	`)
 	if err != nil {
 		return fmt.Errorf("failed to sync counters: %w", err)
@@ -1400,7 +1416,12 @@ func (s *SQLiteStorage) DeleteIssue(ctx context.Context, id string) error {
 		return fmt.Errorf("issue not found: %s", id)
 	}
 
-	return tx.Commit()
+	if err := tx.Commit(); err != nil {
+		return err
+	}
+
+	// Sync counters after deletion to keep them accurate
+	return s.SyncAllCounters(ctx)
 }
 
 // DeleteIssuesResult contains statistics about a batch deletion operation
@@ -1612,6 +1633,11 @@ func (s *SQLiteStorage) DeleteIssues(ctx context.Context, ids []string, cascade
 		return nil, fmt.Errorf("failed to commit transaction: %w", err)
 	}
 
+	// Sync counters after deletion to keep them accurate
+	if err := s.SyncAllCounters(ctx); err != nil {
+		return nil, fmt.Errorf("failed to sync counters after deletion: %w", err)
+	}
+
 	return result, nil
 }