Use pbkdf2 instead of md5, add salt in totp

models/auth/twofactor.go

@@ -52,6 +52,8 @@ type TwoFactor struct {
 	ID               int64 `xorm:"pk autoincr"`
 	UID              int64 `xorm:"UNIQUE"`
 	Secret           string
+	SecretSalt       string
+	SecretAlgo       string
 	ScratchSalt      string
 	ScratchHash      string
 	LastUsedPasscode string             `xorm:"VARCHAR(10)"`
@@ -92,14 +94,38 @@ func (t *TwoFactor) VerifyScratchToken(token string) bool {
 	return subtle.ConstantTimeCompare([]byte(t.ScratchHash), []byte(tempHash)) == 1
 }
 
-func (t *TwoFactor) getEncryptionKey() []byte {
-	k := md5.Sum([]byte(setting.SecretKey))
-	return k[:]
+const (
+	totpSecretKeyIterations = 10000
+	totpSecretKeyLength     = 32
+	totpSecretSaltSize      = 16
+)
+
+func (t *TwoFactor) getEncryptionKey() ([]byte, bool) {
+	if t.SecretAlgo == "" || t.SecretAlgo == "md5" || t.SecretSalt == "" {
+		k := md5.Sum([]byte(setting.SecretKey))
+		return k[:], true
+	}
+	key := pbkdf2.Key([]byte(setting.SecretKey), []byte(t.SecretSalt), totpSecretKeyIterations, totpSecretKeyLength, sha256.New)
+	return key, false
+}
+
+func (t *TwoFactor) rotateSecretSalt() error {
+	saltBytes, err := util.CryptoRandomBytes(totpSecretSaltSize)
+	if err != nil {
+		return err
+	}
+	t.SecretSalt = hex.EncodeToString(saltBytes)
+	t.SecretAlgo = "pbkdf2"
+	return nil
 }
 
 // SetSecret sets the 2FA secret.
 func (t *TwoFactor) SetSecret(secretString string) error {
-	secretBytes, err := secret.AesEncrypt(t.getEncryptionKey(), []byte(secretString))
+	if err := t.rotateSecretSalt(); err != nil {
+		return err
+	}
+	key, _ := t.getEncryptionKey()
+	secretBytes, err := secret.AesEncrypt(key, []byte(secretString))
 	if err != nil {
 		return err
 	}
@@ -108,17 +134,31 @@ func (t *TwoFactor) SetSecret(secretString string) error {
 }
 
 // ValidateTOTP validates the provided passcode.
-func (t *TwoFactor) ValidateTOTP(passcode string) (bool, error) {
+func (t *TwoFactor) ValidateTOTP(passcode string) (bool, bool, error) {
 	decodedStoredSecret, err := base64.StdEncoding.DecodeString(t.Secret)
 	if err != nil {
-		return false, fmt.Errorf("ValidateTOTP invalid base64: %w", err)
+		return false, false, fmt.Errorf("ValidateTOTP invalid base64: %w", err)
 	}
-	secretBytes, err := secret.AesDecrypt(t.getEncryptionKey(), decodedStoredSecret)
+	key, legacyKey := t.getEncryptionKey()
+	secretBytes, err := secret.AesDecrypt(key, decodedStoredSecret)
 	if err != nil {
-		return false, fmt.Errorf("ValidateTOTP unable to decrypt (maybe SECRET_KEY is wrong): %w", err)
+		return false, false, fmt.Errorf("ValidateTOTP unable to decrypt (maybe SECRET_KEY is wrong): %w", err)
 	}
 	secretStr := string(secretBytes)
-	return totp.Validate(passcode, secretStr), nil
+	ok := totp.Validate(passcode, secretStr)
+	if ok && legacyKey {
+		if err := t.rotateSecretSalt(); err != nil {
+			return ok, false, err
+		}
+		key, _ = t.getEncryptionKey()
+		secretBytes, err = secret.AesEncrypt(key, []byte(secretStr))
+		if err != nil {
+			return ok, false, err
+		}
+		t.Secret = base64.StdEncoding.EncodeToString(secretBytes)
+		return ok, true, nil
+	}
+	return ok, false, nil
 }
 
 // NewTwoFactor creates a new two-factor authentication token.

models/auth/twofactor_test.go

@@ -0,0 +1,68 @@
+// Copyright 2026 The Gitea Authors. All rights reserved.
+// SPDX-License-Identifier: MIT
+
+package auth_test
+
+import (
+	"crypto/md5"
+	"encoding/base64"
+	"testing"
+	"time"
+
+	auth_model "code.gitea.io/gitea/models/auth"
+	"code.gitea.io/gitea/modules/secret"
+	"code.gitea.io/gitea/modules/setting"
+
+	"github.com/pquerna/otp/totp"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+func TestTwoFactorSetSecretUsesPBKDF2(t *testing.T) {
+	oldSecretKey := setting.SecretKey
+	setting.SecretKey = "twofactor-test-secret"
+	defer func() {
+		setting.SecretKey = oldSecretKey
+	}()
+
+	secretStr := "JBSWY3DPEHPK3PXP"
+	twofa := &auth_model.TwoFactor{}
+	require.NoError(t, twofa.SetSecret(secretStr))
+
+	assert.NotEmpty(t, twofa.SecretSalt)
+	assert.Equal(t, "pbkdf2", twofa.SecretAlgo)
+
+	passcode, err := totp.GenerateCode(secretStr, time.Now())
+	require.NoError(t, err)
+
+	ok, upgraded, err := twofa.ValidateTOTP(passcode)
+	require.NoError(t, err)
+	assert.True(t, ok)
+	assert.False(t, upgraded)
+}
+
+func TestTwoFactorLegacySecretUpgrade(t *testing.T) {
+	oldSecretKey := setting.SecretKey
+	setting.SecretKey = "twofactor-test-secret"
+	defer func() {
+		setting.SecretKey = oldSecretKey
+	}()
+
+	secretStr := "JBSWY3DPEHPK3PXP"
+	legacyKey := md5.Sum([]byte(setting.SecretKey))
+	ciphertext, err := secret.AesEncrypt(legacyKey[:], []byte(secretStr))
+	require.NoError(t, err)
+	legacySecret := base64.StdEncoding.EncodeToString(ciphertext)
+
+	twofa := &auth_model.TwoFactor{Secret: legacySecret}
+	passcode, err := totp.GenerateCode(secretStr, time.Now())
+	require.NoError(t, err)
+
+	ok, upgraded, err := twofa.ValidateTOTP(passcode)
+	require.NoError(t, err)
+	assert.True(t, ok)
+	assert.True(t, upgraded)
+	assert.NotEmpty(t, twofa.SecretSalt)
+	assert.Equal(t, "pbkdf2", twofa.SecretAlgo)
+	assert.NotEqual(t, legacySecret, twofa.Secret)
+}

models/migrations/migrations.go

@@ -404,6 +404,7 @@ func prepareMigrationTasks() []*migration {
 		newMigration(327, "Add disabled state to action runners", v1_26.AddDisabledToActionRunner),
 		newMigration(328, "Add TokenPermissions column to ActionRunJob", v1_26.AddTokenPermissionsToActionRunJob),
 		newMigration(329, "Add unique constraint for user badge", v1_26.AddUniqueIndexForUserBadge),
+		newMigration(330, "Add secret_salt and secret_algo to two_factor", v1_26.AddSecretSaltToTwoFactor),
 	}
 	return preparedMigrations
 }

models/migrations/v1_26/v330.go

@@ -0,0 +1,21 @@
+// Copyright 2026 The Gitea Authors. All rights reserved.
+// SPDX-License-Identifier: MIT
+
+package v1_26
+
+import "xorm.io/xorm"
+
+// AddSecretSaltToTwoFactor adds a per-user salt column for TOTP secrets.
+func AddSecretSaltToTwoFactor(x *xorm.Engine) error {
+	type TwoFactor struct {
+		SecretSalt string
+		SecretAlgo string
+	}
+
+	if err := x.Sync(new(TwoFactor)); err != nil {
+		return err
+	}
+
+	_, err := x.Exec("UPDATE two_factor SET secret_algo = 'md5' WHERE secret_algo = '' OR secret_algo IS NULL")
+	return err
+}

models/migrations/v1_26/v330_test.go

@@ -0,0 +1,31 @@
+// Copyright 2026 The Gitea Authors. All rights reserved.
+// SPDX-License-Identifier: MIT
+
+package v1_26
+
+import (
+	"testing"
+
+	"code.gitea.io/gitea/models/migrations/base"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+func Test_AddSecretSaltToTwoFactor(t *testing.T) {
+	type TwoFactor struct {
+		ID     int64 `xorm:"pk autoincr"`
+		UID    int64 `xorm:"UNIQUE"`
+		Secret string
+	}
+
+	x, deferrable := base.PrepareTestEnv(t, 0, new(TwoFactor))
+	defer deferrable()
+
+	require.NoError(t, AddSecretSaltToTwoFactor(x))
+
+	table := base.LoadTableSchemasMap(t, x)["two_factor"]
+	require.NotNil(t, table)
+	assert.NotNil(t, table.GetColumn("secret_salt"))
+	assert.NotNil(t, table.GetColumn("secret_algo"))
+}

routers/web/auth/2fa.go

@@ -59,7 +59,7 @@ func TwoFactorPost(ctx *context.Context) {
 	}
 
 	// Validate the passcode with the stored TOTP secret.
-	ok, err := twofa.ValidateTOTP(form.Passcode)
+	ok, _, err := twofa.ValidateTOTP(form.Passcode)
 	if err != nil {
 		ctx.ServerError("UserSignIn", err)
 		return

routers/web/auth/password.go

@@ -177,7 +177,7 @@ func ResetPasswdPost(ctx *context.Context) {
 			regenerateScratchToken = true
 		} else {
 			passcode := ctx.FormString("passcode")
-			ok, err := twofa.ValidateTOTP(passcode)
+			ok, _, err := twofa.ValidateTOTP(passcode)
 			if err != nil {
 				ctx.HTTPError(http.StatusInternalServerError, "ValidateTOTP", err.Error())
 				return

services/auth/basic.go

@@ -175,11 +175,18 @@ func validateTOTP(req *http.Request, u *user_model.User) error {
 		}
 		return err
 	}
-	if ok, err := twofa.ValidateTOTP(req.Header.Get("X-Gitea-OTP")); err != nil {
+	ok, upgraded, err := twofa.ValidateTOTP(req.Header.Get("X-Gitea-OTP"))
+	if err != nil {
 		return err
-	} else if !ok {
+	}
+	if !ok {
 		return util.NewInvalidArgumentErrorf("invalid provided OTP")
 	}
+	if upgraded {
+		if err := auth_model.UpdateTwoFactor(req.Context(), twofa); err != nil {
+			return err
+		}
+	}
 	return nil
 }