PKI vs. FIDO for Passwordless Authentication: What’s the Difference?

Last updated on July 17, 2025

Passwordless authentication is revolutionizing how organizations secure access to networks and services. Two leading technologies in this space are PKI (Public Key Infrastructure) and FIDO (Fast Identity Online). Understanding the differences between PKI and FIDO can help you decide which solution best fits your organization’s needs. Read on to discover more about PKI vs. FIDO.

TL;DR – Key Takeaways

• Both options scrap passwords and block most phishing scams. Smart cards (PKI) and passkeys (FIDO) are phishing-resistant. Both use strong cryptography to prove who you are without sending a secret that hackers can steal.
• Smart cards shine in tightly controlled environments. They’re perfect if you already issue employee ID cards or must meet strict digital‑signature rules, but they need card readers and ongoing certificate upkeep.
• FIDO security keys & passkeys are quicker to roll out for web and mobile apps. Your phone or laptop creates a private key on the spot, so there’s no paperwork or certificate management, and new cloud‑sync features let you move software-bound passkeys between devices.
• Many organisations mix and match. Keep smart cards or hardware-bound FIDO security keys for high‑security logins, and use software-bound synced passkeys for customers or mobile staff who need a faster sign‑in experience.

From PIV & CAC to Passkeys: How PKI and FIDO Differ in Public‑Key Architecture

One of the most significant implementations of PKI is in government-issued identification cards. The U.S. federal government uses PIV cards, while the Department of Defense uses CAC cards. Just like PKI, FIDO also uses asymmetric public‑key cryptography, but it replaces the X.509 certificate hierarchy with a new model in which every relying party (service) gets its own key‑pair created locally by the authenticator, so no user‑ or service‑certificates from an external CA are required. Instead, FIDO introduces new specifications, like WebAuthn and CTAP2, which enable features such as passkeys to simplify authentication.

PKI vs. FIDO: What’s the Difference?

The main difference between PKI and FIDO is that while both use asymmetric cryptography and public/private key pairs, PKI relies on digital certificates issued by Certificate Authorities (CAs) for authentication. In contrast, FIDO uses unique key pairs for each service without needing certificates from external CAs. This makes FIDO more user-friendly and reduces the complexity and cost associated with managing digital certificates.

But there’s more to consider than just that.

Here’s a handy table that outlines the most important differences between PKI and FIDO.

PKI vs. FIDO: Differences Table

Feature	PKI (Public Key Infrastructure)	FIDO (Fast Identity Online)
Authentication Method	PKI uses digital certificates issued by trusted Certificate Authorities (CAs).	FIDO generates unique key pairs for each service.
Key Storage	In public key infrastructure, private keys are stored securely on the user’s device or hardware tokens like smart cards.	In FIDO, private keys are stored on user devices like security keys or smartphones, often secured with biometrics like fingerprints or facial recognition.
Passkey Support	PKI does not natively support passkeys; key management is handled through X.509 certificates.	FIDO supports passkeys, which are FIDO credentials stored on devices like smartphones, enhancing accessibility and convenience for users.
Biometric Authentication	Many PKI deployments embed optional biometric verification, e.g., U.S. PIV/CAC cards support both on‑card and off‑card fingerprint or iris checks, so biometric support is implementation‑specific.	Whether a FIDO authenticator uses biometrics, a PIN, or simple “user‑presence” touch depends on the specific device (e.g., Windows Hello vs. a security key with only a button); biometrics are optional, not mandatory, in the FIDO standard.
Management	PKI is centrally managed through CAs and enterprise infrastructure; IT teams can oversee certificate lifecycle management via a centralized console.	FIDO is based on decentralized management; keys are managed per service and stored on user devices; however, modern MFA platforms like Rublon MFA can provide centralized administration of FIDO keys.
Management Complexity and Cost	PKI certificates need to be managed, renewed, and sometimes revoked, which can add complexity and cost.	FIDO removes enterprise‑issued user certificates; relying parties trust the authenticator’s attestation certificate via the FIDO Metadata Service, so only vendor‑side cert updates remain.
Trust Model	PKI relies on a hierarchical trust model established through trusted third-party CAs; it uses certificate chains and mutual trust relationships.	FIDO establishes trust individually between users and services using unique key pairs (scoped keys); minimizes the impact of breaches and enhances user privacy.
Customization and Integration	PKI requires careful planning and deployment; it offers extensive capabilities beyond authentication, including encryption and digital signatures.	FIDO is easier and faster to implement; benefits from broad support by major tech manufacturers; seamless integration with web and mobile applications, including native support for passkeys.
Use Cases	PKI is ideal for organizations needing comprehensive security solutions, including authentication, encryption, and digital signatures.	FIDO is suited for organizations seeking quick deployment of passwordless authentication or multi-factor authentication with enhanced user experience, especially in web and mobile environments using passkeys.
Standards and Support	PKI is based on open standards like X.509 for digital certificates with extensive native support across operating systems, browsers, and applications; system-agnostic.	FIDO is an open standard from the FIDO Alliance with growing support; benefits from close collaboration between ecosystem players for a consistent user experience.
Additional Capabilities	PKI supports data encryption and digital signatures in addition to authentication; versatile across various security needs.	FIDO’s primary focus is authentication; it aims to eliminate passwords and simplify user verification processes. Passkeys enhance accessibility and ease of use.
Compliance	PKI is suitable for achieving the highest Authenticator Assurance Level 3 (AAL3) defined by NIST SP 800-63 and ISO/IEC 29115 LoA4 for eIDAS identity assurance HIGH when using hardware-based solutions.	FIDO can achieve high assurance levels like AAL3 and eIDAS LoA4 when using hardware-backed authenticators (e.g., hardware security keys or devices with secure elements). Software-bound passkeys without hardware backing and single-factor authenticators are AAL2.
Privacy Considerations	In PKI, users can use certificates across multiple services, but privacy depends on implementation and policies.	FIDO enhances privacy by preventing cross-service tracking through unique key pairs for each service (scoped keys); passkeys stored on personal devices add another layer of privacy.

Advantages of PKI Over FIDO

Here are some reasons why PKI might be a better passwordless choice than FIDO:

• Versatility: PKI can be used for a variety of security needs beyond authentication, such as secure email, code signing, and document signing. This versatility makes it a comprehensive solution for many security requirements.
• Comprehensive Security Functions: PKI offers a wide range of security functions, including authentication, encryption, and digital signatures, which can be applied across networks and applications.
• Centralized Management: PKI enables IT teams to manage certificates and keys centrally, providing robust auditing and lifecycle management. This centralization can simplify administration and enhance security oversight.
• Established Infrastructure: PKI leverages existing security infrastructure and standards, which can be particularly beneficial for organizations already using PKI for other purposes. This can lead to cost savings and easier integration.

Advantages of FIDO Over PKI

Here’s why FIDO might be preferable for passwordless authentication to PKI:

• Privacy Protection: FIDO prevents cross-service tracking of users through the use of scoped keys. Passkeys stored on personal devices further enhance privacy by keeping authentication data under the user’s control.
• Enhanced User Experience: FIDO simplifies authentication by eliminating the need for passwords and using biometrics and passkeys, making the process easy and intuitive for users.
• Quick Implementation: FIDO offers faster deployment with broad support from major tech providers like Apple, Google, and Microsoft, which helps in quick and seamless integration.
• Passkey Support: FIDO supports storing credentials on devices as passkeys, enhancing accessibility and enabling users to authenticate across multiple devices effortlessly.*
• Decentralized Trust Model: FIDO reduces risk by generating unique key pairs for each service, minimizing the impact of a breach on one service from affecting others.

* Passkeys sync only inside the same platform ecosystem (iCloud Keychain, Google Password Manager, etc.). Moving a passkey between different ecosystems still requires re‑registration or a roaming hardware key. Cross‑ecosystem portability is limited today.

Case Studies in Practice

Real‑world deployments in government, banking, and national ID programs show how passwordless authentication works at scale, whether you choose FIDO passkeys or PKI smart cards.

FIDO Deployments

• USDA (U.S. Department of Agriculture) – rolled out FIDO security keys to ~40,000 staff who could not reliably use PIV cards, reporting zero credential‑phishing incidents since deployment. Read the case study.
• ABANCA (Spain) – its mobile app “ABANCA Key” protects 1.2 million customers; in seven months, the bank secured 11 million+ high‑risk transactions and achieved a Customer Effort Score of 4.7. Read the case study.

PKI Deployments

• U.S. Department of Defense – Common Access Card (CAC) – more than 17 million PKI‑enabled smart cards issued to service members, civilians, and contractors, securing physical and logical access at 1,000+ sites worldwide. Read the case study.
• Estonia National eID – compulsory PKI smart card and Mobile ID for 1.3 million citizens; 94 % of income‑tax returns and 25 % of parliamentary votes are completed online via the e‑ID ecosystem. Read the case study.

Free FIDO-Compatible MFA Trial →

Which One Should You Choose?

The choice between PKI and FIDO for passwordless authentication depends on your organization’s specific needs and existing infrastructure.

Consider Using PKI if:

• You already use PKI certificates for encryption, digital signatures, or server authentication.
• You need a comprehensive security solution that includes centralized management and auditing capabilities.
• You require strict identity management protocols or plan to accept external identities via federation.

Consider Using FIDO if:

• You are investing in modern authentication backends that support centralized administration of FIDO credentials across multiple applications.
• You are looking for a faster and more straightforward implementation of passwordless authentication.
• You want to enhance user experience with biometrics and passkeys for simplified login processes.

FIDO vs. PKI: Summary

In summary, both PKI and FIDO offer robust solutions for passwordless authentication. PKI provides a comprehensive security framework with centralized management, suitable for organizations with extensive security needs. FIDO focuses on enhancing user experience through passkeys and biometrics, ideal for quick deployment in modern applications. Understanding the distinctions between PKI vs. FIDO helps you select the solution that best aligns with your security objectives and user experience priorities.