diff --git a/packages/better-auth/src/plugins/two-factor/two-factor.test.ts b/packages/better-auth/src/plugins/two-factor/two-factor.test.ts
index 441ef2b07f..858c91939e 100644
--- a/packages/better-auth/src/plugins/two-factor/two-factor.test.ts
+++ b/packages/better-auth/src/plugins/two-factor/two-factor.test.ts
@@ -322,10 +322,30 @@ describe("two factor", async () => {
 		expect(currentBackupCodes.backupCodes).toBeDefined();
 		expect(currentBackupCodes.backupCodes).not.toContain(backupCode);
 
+		// Start a new 2FA session to test invalid backup code
+		const headers2 = new Headers();
+		await client.signIn.email({
+			email: testUser.email,
+			password: testUser.password,
+			fetchOptions: {
+				onSuccess(context) {
+					const parsed = parseSetCookieHeader(
+						context.response.headers.get("Set-Cookie") || "",
+					);
+					headers2.append(
+						"cookie",
+						`better-auth.two_factor=${
+							parsed.get("better-auth.two_factor")?.value
+						}`,
+					);
+				},
+			},
+		});
+
 		const res = await client.twoFactor.verifyBackupCode({
 			code: "invalid-code",
 			fetchOptions: {
-				headers,
+				headers: headers2,
 				onSuccess(context) {
 					const parsed = parseSetCookieHeader(
 						context.response.headers.get("Set-Cookie") || "",
diff --git a/packages/better-auth/src/plugins/two-factor/verify-two-factor.ts b/packages/better-auth/src/plugins/two-factor/verify-two-factor.ts
index 2def816c63..29c24a7107 100644
--- a/packages/better-auth/src/plugins/two-factor/verify-two-factor.ts
+++ b/packages/better-auth/src/plugins/two-factor/verify-two-factor.ts
@@ -60,10 +60,18 @@ export async function verifyTwoFactor(ctx: GenericEndpointContext) {
 						message: "failed to create session",
 					});
 				}
+				// Delete the verification token from the database after successful verification
+				await ctx.context.internalAdapter.deleteVerificationValue(
+					verificationToken.id,
+				);
 				await setSessionCookie(ctx, {
 					session,
 					user,
 				});
+				// Always clear the two factor cookie after successful verification
+				ctx.setCookie(cookieName.name, "", {
+					maxAge: 0,
+				});
 				if (ctx.body.trustDevice) {
 					const trustDeviceCookie = ctx.context.createAuthCookie(
 						TRUST_DEVICE_COOKIE_NAME,
@@ -89,10 +97,6 @@ export async function verifyTwoFactor(ctx: GenericEndpointContext) {
 					ctx.setCookie(ctx.context.authCookies.dontRememberToken.name, "", {
 						maxAge: 0,
 					});
-					// delete the two factor cookie
-					ctx.setCookie(cookieName.name, "", {
-						maxAge: 0,
-					});
 				}
 				return ctx.json({
 					token: session.token,