How to use Microsoft Authenticator with Remote Desktop

Last updated on February 26, 2025

How do you use Microsoft Authenticator with Remote Desktop (RDP) for secure and convenient access to your remote machines? Multi-Factor Authentication (MFA) is an important measure to ensure the security of your data. Microsoft Authenticator is Microsoft’s MFA authenticator app, and it is gaining popularity as it adds an extra layer of protection and reduces the risk of unauthorized access to your data. In this article, we’ll discuss how to use Microsoft Authenticator with Remote Desktop, how to enable MFA for Remote Desktop Services (RDS), the other MFA for Remote Desktop options, and more. 

Microsoft Authenticator: What it is and how it works

Microsoft Authenticator is Microsoft’s MFA authenticator app that enables a second factor for services that support Time-Based One-Time Passwords (TOTPs). This solution is available on mobile devices and works on the simple principle of ‘Something you know, something you have’. This means that you need to enter your password and also have access to a physical device (e.g., a smartphone) with the Microsoft Authenticator mobile app to access your account. The authentication process works via a 6-digit code you must enter on a login prompt right after entering the password.

The Microsoft Authenticator app securely stores your account details and verifies your identity through biometric factors such as fingerprints or face recognition. To use the Microsoft Authenticator application, you must have a valid Microsoft Account and have the app installed on your device.

Can you use Microsoft Authenticator with RDP?

Yes, you can! Microsoft Authenticator is compatible with Remote Desktop Protocol (RDP). This will allow you to use the Microsoft Authenticator app to authenticate your identity and access your remote machines.

Enabling Microsoft Authenticator MFA for Remote Desktop Services (RDS)

The first step to enabling Microsoft Authenticator with Remote Desktop Services (RDS) is to download and install the Microsoft Authenticator app. Once the app is installed, you must set up Two-Factor Authentication (2FA).

Next, open the Microsoft Authenticator application on your mobile device and set up an account by scanning the QR code that appears on the Rublon Prompt displayed on your Remote Desktop login page.

You can now start your RDP connection and enter the name of the remote computer, the user name, and the password.

After that,  enter the 6-digit code from the Microsoft Authenticator application into your Remote Desktop login page to authenticate your identity.

From now on, you can use 2FA with your Remote Desktop account during each login.

How to enable Multi-Factor Authentication (MFA) for Remote Desktop connections

1. Download the Microsoft Authenticator application on your mobile device.
2. Download Rublon MFA for Windows Logon and RDP or Microsoft Remote Desktop Services (RD Web Access and RD Web Client).
3. Deploy the Rublon MFA for Windows connector on one or more of your endpoints by following the step-by-step instructions.
4. Enroll your third-party authenticator app (Microsoft Authenticator) with Rublon MFA.
5. Start an RDP connection and enter your username and password.
6. Select the Mobile Passcode authentication method from the Rublon Prompt and enter the TOTP generated by Microsoft Authenticator.
7. You gain secure access to Remote Desktop with Microsoft Authenticator MFA.

For more detailed instructions on how to use Microsoft Authenticator with Remote Desktop for MFA, refer to:

How to enroll a third-party authenticator app?

Microsoft Authenticator MFA for Remote Desktop Services (RDS): What are the other options?

You can use other MFA solutions besides Microsoft Authenticator. To enable MFA and 2FA for Remote Desktop Services (RDS), you can use Rublon Authenticator or Google Authenticator. If you choose to enroll a mobile device with Rublon Authenticator, you gain all the following MFA authentication methods:

• SMS Messages: You will receive a 6-digit code via text message (SMS), which you will need to enter when prompted during login.
• Push Notification: You will receive a notification on your mobile device via the Rublon Authenticator mobile app, which can be used as a second-factor authentication.
• QR Code: You will scan a QR Code displayed on the Remote Desktop login screen to gain secure access to your RDP endpoints.
• YubiKey OTP Security Key: You will use your FIDO security key to verify your identity.
• Email Verification: You will receive an email message, which you will have to click to gain access to your RDP endpoint.

Best Microsoft Authenticator Alternative for MFA

Here’s a summary of the benefits of Rublon Multi-Factor Authentication:

• Rublon Authenticator mobile app: With Rublon’s dedicated mobile app, you can receive Mobile Push notifications, use Mobile Passcode (TOTP) or scan a QR code to log in to your applications.
• Third-party authenticator apps: You can enable your users to use third-party authenticator apps, such as Google Authenticator and Microsoft Authenticator.
• Other powerful authentication methods: You can also allow your users to use other authentication methods. For example, Rublon MFA supports FIDO security keys – a phishing-resistant, powerful way to access accounts and Remote Desktop Services (RDS).

Enable Remote Desktop MFA with Microsoft Authenticator

Start a Free 30-Day Rublon Multi-Factor Authentication Trial and enable company-wide MFA for Remote Desktop. Your users will gain an extra layer of login security via multiple authentication methods, including YubiKey OTP, Mobile Push, and Mobile Passcode (TOTP) using Microsoft Authenticator, Google Authenticator, Rublon Authenticator, and more.

Summing up Microsoft Authenticator MFA for Remote Desktop

Microsoft Authenticator is a convenient authenticator app that you can use to secure your Remote Desktop connections with Rublon MFA. To secure your remote connections, you can also use other authenticator apps, such as Rublon Authenticator and Google Authenticator. With Microsoft Authenticator MFA for Remote Desktop Services (RDS), you can rest assured that your data is safe and secure.