diff --git a/internal/api/passkey_authentication.go b/internal/api/passkey_authentication.go
index 6967d3f0a5..eb1ea26029 100644
--- a/internal/api/passkey_authentication.go
+++ b/internal/api/passkey_authentication.go
@@ -137,7 +137,7 @@ func (a *API) PasskeyAuthenticationVerify(w http.ResponseWriter, r *http.Request
 			return nil, models.WebAuthnCredentialNotFoundError{}
 		}
 
-		return newWebAuthnUser(u, creds), nil
+		return newWebAuthnUserWithAssertion(u, creds, parsedResponse), nil
 	}
 
 	webauthnUser, credential, err := webAuthn.ValidatePasskeyLogin(handler, sessionData, parsedResponse)
@@ -179,7 +179,7 @@ func (a *API) PasskeyAuthenticationVerify(w http.ResponseWriter, r *http.Request
 	err = db.Transaction(func(tx *storage.Connection) error {
 		var terr error
 
-		if terr = passkeyCredential.UpdateLastUsedWithSignCount(tx, credential.Authenticator.SignCount); terr != nil {
+		if terr = passkeyCredential.UpdateLastUsedWithSignCountAndFlags(tx, credential.Authenticator.SignCount, credential.Flags.BackupEligible, credential.Flags.BackupState); terr != nil {
 			return terr
 		}
 
diff --git a/internal/api/passkey_virtual_authenticator_test.go b/internal/api/passkey_virtual_authenticator_test.go
index efbd81f1fc..788972db2a 100644
--- a/internal/api/passkey_virtual_authenticator_test.go
+++ b/internal/api/passkey_virtual_authenticator_test.go
@@ -132,6 +132,10 @@ func (va *virtualAuthenticator) createCredential(options *protocol.PublicKeyCred
 // authentication options. It picks the first stored credential (discoverable flow) and signs
 // the authenticator data + client data hash.
 func (va *virtualAuthenticator) getAssertion(options *protocol.PublicKeyCredentialRequestOptions) (*virtualAssertionResponse, error) {
+	return va.getAssertionWithFlags(options, 0x05)
+}
+
+func (va *virtualAuthenticator) getAssertionWithFlags(options *protocol.PublicKeyCredentialRequestOptions, flags byte) (*virtualAssertionResponse, error) {
 	if len(va.credentials) == 0 {
 		return nil, fmt.Errorf("no stored credentials")
 	}
@@ -156,8 +160,6 @@ func (va *virtualAuthenticator) getAssertion(options *protocol.PublicKeyCredenti
 
 	// Build authenticator data for assertion (no attested credential data)
 	rpIDHash := sha256.Sum256([]byte(va.rpID))
-	// flags: UP (bit 0) | UV (bit 2) = 0x05
-	flags := byte(0x05)
 	var authData []byte
 	authData = append(authData, rpIDHash[:]...)
 	authData = append(authData, flags)
diff --git a/internal/api/passkey_webauthn.go b/internal/api/passkey_webauthn.go
index 104eda515c..9cbd23fee7 100644
--- a/internal/api/passkey_webauthn.go
+++ b/internal/api/passkey_webauthn.go
@@ -1,6 +1,8 @@
 package api
 
 import (
+	"bytes"
+
 	"github.com/go-webauthn/webauthn/protocol"
 	"github.com/go-webauthn/webauthn/webauthn"
 	"github.com/supabase/auth/internal/api/apierrors"
@@ -48,10 +50,18 @@ type webAuthnUser struct {
 }
 
 func newWebAuthnUser(user *models.User, passkeyCredentials []*models.WebAuthnCredential) *webAuthnUser {
+	return newWebAuthnUserWithAssertion(user, passkeyCredentials, nil)
+}
+
+func newWebAuthnUserWithAssertion(user *models.User, passkeyCredentials []*models.WebAuthnCredential, assertion *protocol.ParsedCredentialAssertionData) *webAuthnUser {
 	credentials := make([]webauthn.Credential, len(passkeyCredentials))
 
 	for i, pc := range passkeyCredentials {
-		credentials[i] = pc.ToWebAuthnCredential()
+		cred := pc.ToWebAuthnCredential()
+		if assertion != nil && bytes.Equal(pc.CredentialID, assertion.RawID) {
+			cred.Flags.BackupEligible = assertion.Response.AuthenticatorData.Flags.HasBackupEligible()
+		}
+		credentials[i] = cred
 	}
 
 	return &webAuthnUser{
diff --git a/internal/api/passkey_webauthn_test.go b/internal/api/passkey_webauthn_test.go
index 0546e1baa8..fdc74fc20d 100644
--- a/internal/api/passkey_webauthn_test.go
+++ b/internal/api/passkey_webauthn_test.go
@@ -190,3 +190,59 @@ func (ts *PasskeyWebAuthnTestSuite) TestWebAuthnUserWithCredentials() {
 	ts.True(webauthnCreds[1].Flags.BackupEligible)
 	ts.True(webauthnCreds[1].Flags.BackupState)
 }
+
+func (ts *PasskeyWebAuthnTestSuite) TestWebAuthnUserWithAssertionAlignsBackupEligible() {
+	user := &models.User{
+		ID: uuid.Must(uuid.NewV4()),
+	}
+	user.Email = "user@example.com"
+
+	credID := []byte("cred-be-flip")
+	creds := []*models.WebAuthnCredential{
+		{
+			ID:              uuid.Must(uuid.NewV4()),
+			UserID:          user.ID,
+			CredentialID:    credID,
+			PublicKey:       []byte("pk-1"),
+			AttestationType: "none",
+			SignCount:       0,
+			BackupEligible:  false,
+			BackedUp:        false,
+		},
+	}
+
+	assertion := &protocol.ParsedCredentialAssertionData{
+		ParsedPublicKeyCredential: protocol.ParsedPublicKeyCredential{
+			RawID: credID,
+		},
+		Response: protocol.ParsedAssertionResponse{
+			AuthenticatorData: protocol.AuthenticatorData{
+				Flags: protocol.FlagBackupEligible, // BE = true
+			},
+		},
+	}
+
+	wu := newWebAuthnUserWithAssertion(user, creds, assertion)
+	webauthnCreds := wu.WebAuthnCredentials()
+	ts.Require().Len(webauthnCreds, 1)
+
+	// Verify that BackupEligible is updated to true matching assertion
+	ts.True(webauthnCreds[0].Flags.BackupEligible)
+
+	// Non-matching assertion leaves BackupEligible unchanged
+	otherAssertion := &protocol.ParsedCredentialAssertionData{
+		ParsedPublicKeyCredential: protocol.ParsedPublicKeyCredential{
+			RawID: []byte("other-cred-id"),
+		},
+		Response: protocol.ParsedAssertionResponse{
+			AuthenticatorData: protocol.AuthenticatorData{
+				Flags: protocol.FlagBackupEligible,
+			},
+		},
+	}
+
+	wuOther := newWebAuthnUserWithAssertion(user, creds, otherAssertion)
+	webauthnCredsOther := wuOther.WebAuthnCredentials()
+	ts.Require().Len(webauthnCredsOther, 1)
+	ts.False(webauthnCredsOther[0].Flags.BackupEligible)
+}
diff --git a/internal/models/webauthn_credential.go b/internal/models/webauthn_credential.go
index b7dc60e1dc..15e1fc8439 100644
--- a/internal/models/webauthn_credential.go
+++ b/internal/models/webauthn_credential.go
@@ -184,6 +184,15 @@ func (pc *WebAuthnCredential) UpdateLastUsedWithSignCount(tx *storage.Connection
 	return tx.UpdateOnly(pc, "sign_count", "last_used_at", "updated_at")
 }
 
+func (pc *WebAuthnCredential) UpdateLastUsedWithSignCountAndFlags(tx *storage.Connection, signCount uint32, backupEligible, backedUp bool) error {
+	now := time.Now()
+	pc.SignCount = signCount
+	pc.BackupEligible = backupEligible
+	pc.BackedUp = backedUp
+	pc.LastUsedAt = &now
+	return tx.UpdateOnly(pc, "sign_count", "backup_eligible", "backed_up", "last_used_at", "updated_at")
+}
+
 func (pc *WebAuthnCredential) UpdateFriendlyName(tx *storage.Connection, friendlyName string) error {
 	pc.FriendlyName = friendlyName
 	return tx.UpdateOnly(pc, "friendly_name", "updated_at")