diff --git a/cmd/bd/daemon.go b/cmd/bd/daemon.go
index cb6baaa0..13ea819b 100644
--- a/cmd/bd/daemon.go
+++ b/cmd/bd/daemon.go
@@ -452,6 +452,12 @@ func runDaemonLoop(interval time.Duration, autoCommit, autoPush, autoPull, local
 	} else if err := validateDatabaseFingerprint(ctx, store, &log); err != nil {
 		if os.Getenv("BEADS_IGNORE_REPO_MISMATCH") != "1" {
 			log.Error("repository fingerprint validation failed", "error", err)
+			// Write error to daemon-error file so user sees it instead of just "daemon took too long"
+			errFile := filepath.Join(beadsDir, "daemon-error")
+			// nolint:gosec // G306: Error file needs to be readable for debugging
+			if writeErr := os.WriteFile(errFile, []byte(err.Error()), 0644); writeErr != nil {
+				log.Warn("could not write daemon-error file", "error", writeErr)
+			}
 			return // Use return instead of os.Exit to allow defers to run
 		}
 		log.Warn("repository mismatch ignored (BEADS_IGNORE_REPO_MISMATCH=1)")
diff --git a/cmd/bd/daemon_autostart.go b/cmd/bd/daemon_autostart.go
index 97419154..c4afc0d4 100644
--- a/cmd/bd/daemon_autostart.go
+++ b/cmd/bd/daemon_autostart.go
@@ -340,6 +340,17 @@ func startDaemonProcess(socketPath string) bool {
 
 	recordDaemonStartFailure()
 	debugLog("daemon socket not ready after 5 seconds")
+
+	// Check for daemon-error file which contains the actual failure reason
+	beadsDir := filepath.Dir(dbPath)
+	errFile := filepath.Join(beadsDir, "daemon-error")
+	if errContent, err := os.ReadFile(errFile); err == nil && len(errContent) > 0 {
+		// Show the actual error from the daemon
+		fmt.Fprintf(os.Stderr, "%s Daemon failed to start:\n", ui.RenderWarn("Warning:"))
+		fmt.Fprintf(os.Stderr, "%s\n", string(errContent))
+		return false
+	}
+
 	// Emit visible warning so user understands why command was slow
 	fmt.Fprintf(os.Stderr, "%s Daemon took too long to start (>5s). Running in direct mode.\n", ui.RenderWarn("Warning:"))
 	fmt.Fprintf(os.Stderr, "  %s Run 'bd doctor' to diagnose daemon issues\n", ui.RenderMuted("Hint:"))
diff --git a/cmd/bd/doctor/integrity.go b/cmd/bd/doctor/integrity.go
index 07cf4bc8..646cd93e 100644
--- a/cmd/bd/doctor/integrity.go
+++ b/cmd/bd/doctor/integrity.go
@@ -441,12 +441,12 @@ func CheckRepoFingerprint(path string) DoctorCheck {
 	err = db.QueryRow("SELECT value FROM metadata WHERE key = 'repo_id'").Scan(&storedRepoID)
 	if err != nil {
 		if err == sql.ErrNoRows || strings.Contains(err.Error(), "no such table") {
-			// Legacy database without repo_id
+			// Legacy database without repo_id - this is an error because daemon won't start
 			return DoctorCheck{
 				Name:    "Repo Fingerprint",
-				Status:  StatusWarning,
+				Status:  StatusError,
 				Message: "Legacy database (no fingerprint)",
-				Detail:  "Database was created before version 0.17.5",
+				Detail:  "Database was created before version 0.17.5. Daemon will fail to start.",
 				Fix:     "Run 'bd migrate --update-repo-id' to add fingerprint",
 			}
 		}
@@ -458,13 +458,13 @@ func CheckRepoFingerprint(path string) DoctorCheck {
 		}
 	}
 
-	// If repo_id is empty, treat as legacy
+	// If repo_id is empty, treat as legacy - this is an error because daemon won't start
 	if storedRepoID == "" {
 		return DoctorCheck{
 			Name:    "Repo Fingerprint",
-			Status:  StatusWarning,
+			Status:  StatusError,
 			Message: "Legacy database (empty fingerprint)",
-			Detail:  "Database was created before version 0.17.5",
+			Detail:  "Database was created before version 0.17.5. Daemon will fail to start.",
 			Fix:     "Run 'bd migrate --update-repo-id' to add fingerprint",
 		}
 	}