Passkeys vs. Authenticator Apps vs. YubiKeys: Choosing the Right MFA

Multi-factor authentication (MFA) is no longer optional for organizations of any size. However, not all MFA methods deliver the same level of protection. While SMS codes and email-based verification are widely used, they are increasingly vulnerable to phishing and token theft. More advanced solutions—such as passkeys, authenticator apps, and FIDO2 security keys like YubiKeys—offer stronger defenses.

This article compares these modern authentication methods, highlighting their security benefits, adoption challenges, and best-fit use cases to help you choose the right MFA strategy for your organization.

What Are Passkeys?

Passkeys are a passwordless authentication method tied directly to a device. They rely on cryptographic keys stored in hardware, meaning there is no password to steal or code to intercept.

• Security Benefits: Resistant to phishing and credential replay attacks. Passkeys eliminate the reliance on passwords altogether.

• Adoption Challenges: Dependence on compatible devices can complicate rollouts in organizations with a mix of operating systems or older hardware.

• Best Use Cases: General workforce accounts, especially in organizations that prioritize ease of use alongside security.

What Are Authenticator Apps?

Authenticator apps—such as Microsoft Authenticator or Google Authenticator—generate time-based one-time passcodes (TOTPs) or push notifications to verify user identity.

• Security Benefits: More secure than SMS or email codes. Number matching in Microsoft Authenticator adds a layer of protection against push notification fatigue.

• Adoption Challenges: Still vulnerable to real-time phishing attacks that steal session tokens. Users must have mobile devices available and configured properly.

• Best Use Cases: Standard user accounts, organizations seeking an easy and inexpensive upgrade from legacy MFA.

What Are YubiKeys (FIDO2 Security Keys)?

YubiKeys and other FIDO2-based hardware security keys provide the highest level of phishing-resistant MFA. Authentication is tied to the device and cryptographically validated, making it nearly impossible for attackers to intercept or reuse.

• Security Benefits: Gold standard for phishing resistance, immune to token theft, and highly reliable across platforms.

• Adoption Challenges: Hardware costs and distribution logistics. Requires user training and device management.

• Best Use Cases: High-sensitivity accounts such as administrators, executives, finance teams, and users with access to regulated or confidential data.

Choosing the Right MFA for Your Organization

There is no one-size-fits-all solution. The right MFA strategy often combines multiple methods:

• Baseline Protection: Authenticator apps provide a strong improvement over SMS codes.

• Workforce-Friendly: Passkeys balance security with ease of use, making them ideal for widespread adoption.

• High-Security Accounts: YubiKeys or other FIDO2 keys should be mandatory for administrators and privileged users.

By layering methods based on account sensitivity, organizations achieve stronger security without creating unnecessary friction for users.

Conclusion

As phishing and token theft continue to evolve, organizations must move beyond legacy MFA. Passkeys, authenticator apps, and YubiKeys each offer distinct advantages, and when used strategically together, they provide comprehensive protection.

The key is matching the right authentication method to the right accounts: authenticator apps for general users, passkeys for broader adoption, and YubiKeys for privileged or high-risk accounts. With this layered approach, your organization can improve both security and user experience.