Multi-factor authentication is a security mechanism that requires additional verification beyond your username (or email) and password. This usually comes in the form of a one-time passcode, a push notification, or plugging in and tapping a hardware security key.

Common protocols

Email and SMS MFA

Email and SMS MFA are examples of the weaker MFA protocols. Email MFA is not great as whoever controls your email account can typically both reset your password and receive your MFA verification. SMS, on the other hand, is problematic due to the lack of any kind of encryption, making it vulnerable to sniffing. Sim swap attacks, if carried out successfully, will allow an attacker to receive your one-time passcode while locking you out of your own account. In certain cases, websites or services may also allow the user to reset their account login by calling them using the phone number used for MFA, which could be faked with a spoofed CallerID.

Only use these protocols when it is the only option you have, and be very careful with SMS MFA as it could actually worsen your security.

Push Confirmations

Push confirmation MFA is typically a notification being sent to an app on your phone asking you to confirm new account logins. This method is a lot better than SMS or email, since an attacker typically wouldn’t be able to get these push notifications without having an already logged-in device.

Push confirmation in most cases relies on a third-party provider like Duo. This means that trust is placed in a server that neither you nor your service provider control. A malicious push confirmation server could compromise your MFA or profile you based on which website and account you use with the service.

Even if the push notification application and server is provided by a first-party as is the case with Microsoft login and Microsoft Authenticator, there is still a risk of you accidentally tapping on the confirmation button.

Time-based One-time Password (TOTP)

TOTP is one of the most common forms of MFA available. When you set up TOTP, you setup a “shared secret” with the service that you intend to use and store it in your authentication app.

The time-limited code is then derived from the shared secret and the current time. As the code is only valid for a short time, without access to the shared secret, an adversary cannot generate new codes.

If you have a YubiKey, you should store the “shared secrets” on the key itself using the Yubico Authenticator app. After the initial setup, the Yubico Authenticator will only expose the 6 digit code to the machine it is running on, but not the shared secret. Additional security can be set up by requiring touch confirmation, protecting digit codes not in used from a compromised operating system.

Unlike WebAuthn, TOTP offers no protection against phishing or reuse attacks. If an adversary obtains a valid code from you, they may use it as many times as they like until it expires (generally 30 seconds + grace period).

Despite its short comings, we consider TOTP better and safer than Push Confirmations.

Yubico OTP

Yubico OTP is an authentication protocol typically implemented in hardware security keys. When you decide to use Yubico OTP, the key will generate a public ID, private ID, and a Secret Key which is then uploaded to the Yubico OTP server.

When logging into a website, all you need to do is to physically touch the security key. The security key will emulate a keyboard and print out a one-time password into the password field.

The service will then forward the one-time password to the Yubico OTP server for validation. A counter is incremented both on the key and Yubico’s validation server. The OTP can only be used once, and when a successful authentication occurs, the counter is increased which prevents reuse of the OTP. Yubico provides a detailed document about the process.

Yubico OTP

The Yubico validation server is a cloud based service, and you’re placing trust in Yubico that their server won’t be used to bypass your MFA or profile you. The public ID associated with Yubico OTP is reused on every website and could be another avenue for third-parties to profile you. Like TOTP, Yubico OTP does not provide phishing resistance.

Yubico OTP is an inferior protocol compared to TOTP since TOTP does not need trust in a third-party server and most security keys that support Yubico OTP (namely the YubiKey and OnlyKey) supports TOTP anyway. Yubico OTP is still better than Push Confirmation, however.

FIDO2 (Fast IDentity Online)

FIDO includes a number of standards; first there was U2F and then later FIDO2 which includes the web standard WebAuthn.

U2F and FIDO2 refer to the Client to Authenticator Protocol, which is the protocol between the security key and the computer, such as a laptop or phone. It complements WebAuthn which is the component used to authenticate with the website (the “Relying Party”) you’re trying to log in on.

WebAuthn is the most secure and private form of second factor authentication. While the authentication experience is similar to Yubico OTP, the key does not print out a one-time password and validate with a third-party server. Instead, it uses public key cryptography for authentication.

Since FIDO2/WebAuthn uses unique cryptographic keys with each internet site, a site pretending to be another one will not be able to get the correct response to the challenge for MFA, making FIDO2/Webauthn is invulnerable phising. It is also because of this authentication mechanism that a physical FIDO2 security key is not identifiable across different services like Yubico OTP. Even better, FIDO2 uses a counter for each authentication, which would help with detecting cloned keys.

If a website or service supports WebAuthn for the authentication, it is highly recommended that you use it over any other form of MFA.


Initial Set Up

When buying a security key, it is important that you change the default credentials, set up password protection for the key, and enable touch confirmation if your key supports it. Products such as the YubiKey have multiple interfaces with separate credentials for each one of them, so you should go over each interface and set up protection as well.


You should always have backups for your MFA method. Hardware security keys can get lost, stolen, or simply stop working over time. It is recommended that you have a pair of hardware security keys with the same access to your accounts instead of just one.

When using TOTP with an authenticator app, be sure to back up your recovery keys to an offline and encrypted storage device.

You are only as secure as the weakest authentication method you use. For instance, it makes little sense to add SMS 2FA as an alternative MFA method if you are already using FIDO2. An adversary who can compromise your SMS 2FA will get into your account just as easily as if you didn’t use FIDO2 at all.

Thus, it is important to stick to the best authentication method you have access to. It is better to have 2 Yubikeys for FIDO2 than 1 FIDO2 key and one authenticator app for TOTP. Likewise, it is better to have 1 TOTP instance and a backup key than to use TOTP alongside with Email or SMS 2FA.