diff --git a/cmd/bd/doctor/sync_divergence.go b/cmd/bd/doctor/sync_divergence.go
index 4371dcd4..4c76a9f2 100644
--- a/cmd/bd/doctor/sync_divergence.go
+++ b/cmd/bd/doctor/sync_divergence.go
@@ -180,7 +180,7 @@ func checkSQLiteMtimeDivergence(path, beadsDir string) *SyncDivergenceIssue {
 	defer db.Close()
 
 	var lastImportTimeStr string
-	err = db.QueryRow("SELECT value FROM config WHERE key = 'last_import_time'").Scan(&lastImportTimeStr)
+	err = db.QueryRow("SELECT value FROM metadata WHERE key = 'last_import_time'").Scan(&lastImportTimeStr)
 	if err != nil {
 		// No last_import_time recorded - this is a potential issue
 		return &SyncDivergenceIssue{
diff --git a/cmd/bd/doctor/sync_divergence_test.go b/cmd/bd/doctor/sync_divergence_test.go
index c9a515cf..79fa6b28 100644
--- a/cmd/bd/doctor/sync_divergence_test.go
+++ b/cmd/bd/doctor/sync_divergence_test.go
@@ -150,7 +150,7 @@ func TestCheckSQLiteMtimeDivergence(t *testing.T) {
 			t.Fatal(err)
 		}
 		_, _ = db.Exec("CREATE TABLE issues (id TEXT)")
-		_, _ = db.Exec("CREATE TABLE config (key TEXT, value TEXT)")
+		_, _ = db.Exec("CREATE TABLE metadata (key TEXT, value TEXT)")
 		db.Close()
 
 		issue := checkSQLiteMtimeDivergence(dir, beadsDir)
@@ -173,7 +173,7 @@ func TestCheckSQLiteMtimeDivergence(t *testing.T) {
 			t.Fatal(err)
 		}
 		_, _ = db.Exec("CREATE TABLE issues (id TEXT)")
-		_, _ = db.Exec("CREATE TABLE config (key TEXT, value TEXT)")
+		_, _ = db.Exec("CREATE TABLE metadata (key TEXT, value TEXT)")
 		db.Close()
 
 		// Create JSONL
@@ -214,8 +214,8 @@ func TestCheckSQLiteMtimeDivergence(t *testing.T) {
 			t.Fatal(err)
 		}
 		_, _ = db.Exec("CREATE TABLE issues (id TEXT)")
-		_, _ = db.Exec("CREATE TABLE config (key TEXT, value TEXT)")
-		_, _ = db.Exec("INSERT INTO config (key, value) VALUES (?, ?)",
+		_, _ = db.Exec("CREATE TABLE metadata (key TEXT, value TEXT)")
+		_, _ = db.Exec("INSERT INTO metadata (key, value) VALUES (?, ?)",
 			"last_import_time", importTime.Format(time.RFC3339))
 		db.Close()
 
@@ -239,9 +239,9 @@ func TestCheckSQLiteMtimeDivergence(t *testing.T) {
 			t.Fatal(err)
 		}
 		_, _ = db.Exec("CREATE TABLE issues (id TEXT)")
-		_, _ = db.Exec("CREATE TABLE config (key TEXT, value TEXT)")
+		_, _ = db.Exec("CREATE TABLE metadata (key TEXT, value TEXT)")
 		oldTime := time.Now().Add(-1 * time.Hour)
-		_, _ = db.Exec("INSERT INTO config (key, value) VALUES (?, ?)",
+		_, _ = db.Exec("INSERT INTO metadata (key, value) VALUES (?, ?)",
 			"last_import_time", oldTime.Format(time.RFC3339))
 		db.Close()
 
@@ -263,6 +263,47 @@ func TestCheckSQLiteMtimeDivergence(t *testing.T) {
 			}
 		}
 	})
+
+	// Regression test: verify we read from metadata table, not config table.
+	// The sync code writes to metadata, so doctor must read from there.
+	// This catches the bug where doctor queried 'config' instead of 'metadata'.
+	t.Run("reads from metadata table not config", func(t *testing.T) {
+		dir := mkTmpDirInTmp(t, "bd-mtime-table-*")
+		beadsDir := filepath.Join(dir, ".beads")
+		if err := os.MkdirAll(beadsDir, 0755); err != nil {
+			t.Fatal(err)
+		}
+
+		// Create JSONL first
+		jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+		if err := os.WriteFile(jsonlPath, []byte(`{"id":"test-1"}`+"\n"), 0644); err != nil {
+			t.Fatal(err)
+		}
+
+		// Get JSONL mtime
+		jsonlInfo, _ := os.Stat(jsonlPath)
+		importTime := jsonlInfo.ModTime()
+
+		// Create database with BOTH config and metadata tables (realistic schema)
+		// Put last_import_time ONLY in metadata (as real sync code does)
+		dbPath := filepath.Join(beadsDir, "beads.db")
+		db, err := sql.Open("sqlite3", dbPath)
+		if err != nil {
+			t.Fatal(err)
+		}
+		_, _ = db.Exec("CREATE TABLE issues (id TEXT)")
+		_, _ = db.Exec("CREATE TABLE config (key TEXT, value TEXT)")
+		_, _ = db.Exec("CREATE TABLE metadata (key TEXT, value TEXT)")
+		// Only insert into metadata, NOT config
+		_, _ = db.Exec("INSERT INTO metadata (key, value) VALUES (?, ?)",
+			"last_import_time", importTime.Format(time.RFC3339))
+		db.Close()
+
+		issue := checkSQLiteMtimeDivergence(dir, beadsDir)
+		if issue != nil {
+			t.Errorf("expected nil issue when last_import_time is in metadata table, got %+v", issue)
+		}
+	})
 }
 
 func TestCheckUncommittedBeadsChanges(t *testing.T) {