diff --git a/server/services/setup/db.go b/server/services/setup/db.go
index 7633184..4e59343 100644
--- a/server/services/setup/db.go
+++ b/server/services/setup/db.go
@@ -252,6 +252,7 @@ func SetDatabaseSettingsWithOptions(ctx *context.Context, settings DatabaseSetti
 
 	previousConfig := *configData
 	candidateConfig := *configData
+	markSetupInProgress(&candidateConfig)
 	candidateConfig.DbType = dbType
 	candidateConfig.DbDSN = dbDSN
 	if err = config.WriteConfig(&candidateConfig); err != nil {
@@ -269,6 +270,16 @@ func SetDatabaseSettingsWithOptions(ctx *context.Context, settings DatabaseSetti
 	return nil
 }
 
+func markSetupInProgress(cfg *config.Config) {
+	if cfg == nil {
+		return
+	}
+	cfg.IsInit = false
+	if !cfg.SetupState.Valid() {
+		cfg.SetupState = config.SetupStateBootstrap
+	}
+}
+
 func closeDatabaseInstance() {
 	if db.Instance == nil {
 		return
diff --git a/server/services/setup/db_database_test.go b/server/services/setup/db_database_test.go
index 0146326..df4e9a5 100644
--- a/server/services/setup/db_database_test.go
+++ b/server/services/setup/db_database_test.go
@@ -10,10 +10,37 @@ import (
 	"testing"
 	"time"
 
+	"git.pcux.cn/xuans/Smail/config"
 	"github.com/go-sql-driver/mysql"
 	"github.com/lib/pq"
 )
 
+func TestMarkSetupInProgressClearsLegacyInitializationFlag(t *testing.T) {
+	cfg := &config.Config{IsInit: true}
+
+	markSetupInProgress(cfg)
+
+	if cfg.IsInit {
+		t.Fatal("legacy initialization flag must be cleared during setup")
+	}
+	if cfg.SetupState != config.SetupStateBootstrap {
+		t.Fatalf("setup state = %q, want %q", cfg.SetupState, config.SetupStateBootstrap)
+	}
+}
+
+func TestMarkSetupInProgressPreservesExplicitSetupState(t *testing.T) {
+	cfg := &config.Config{IsInit: true, SetupState: config.SetupStateNew}
+
+	markSetupInProgress(cfg)
+
+	if cfg.IsInit {
+		t.Fatal("legacy initialization flag must be cleared during setup")
+	}
+	if cfg.SetupState != config.SetupStateNew {
+		t.Fatalf("setup state = %q, want %q", cfg.SetupState, config.SetupStateNew)
+	}
+}
+
 type fakeSetupDB struct {
 	pingErrors  []error
 	pingCalls   int
diff --git a/server/services/setup/domain.go b/server/services/setup/domain.go
index 717af9b..4ad289e 100644
--- a/server/services/setup/domain.go
+++ b/server/services/setup/domain.go
@@ -21,6 +21,7 @@ func SetDomainSettings(smtpDomain, webDomain, multiDomains string) error {
 	if err != nil {
 		return errors.Wrap(err)
 	}
+	markSetupInProgress(configData)
 
 	smtpDomain, err = validation.NormalizeDomain(smtpDomain)
 	if err != nil {