What is the difference between passkeys and one-time passwords for secure sign-in?

Passkeys are phishing-resistant credentials that use public key cryptography and are bound to a user device or authenticator. One-time passwords are temporary codes sent by SMS, email, or an app, and they can still be intercepted, relayed, or phished. For security teams, passkeys usually provide stronger protection and a cleaner user experience.

Passkeys and one-time passwords both help users sign in without typing a traditional password, but they protect against different failure modes. Passkeys are built around public key cryptography and device-bound authentication, which makes them much harder to phish or relay. One-time passwords are temporary shared secrets, so they still depend on the user correctly handling a code that can be intercepted, forwarded, or tricked out of them.

That distinction matters because many sign-in incidents are not about breaking encryption; they are about abusing the authentication step itself. A phishing page can capture an OTP in real time and reuse it immediately, while a passkey response is tied to the legitimate origin and the user’s authenticator. For teams deciding how to reduce account takeover, the question is not only convenience, but whether the factor resists live adversary interaction.

Passkeys also change the operational model. They shift trust away from remembered secrets and toward managed authenticators, which is a stronger fit for modern credential hygiene. By contrast, OTPs remain useful as a fallback or migration bridge, but they do not eliminate the core weaknesses of out-of-band codes. In practice, many teams discover the gap only after repeated phishing or relay attempts have already demonstrated that the code was the easiest part to steal.

How the Authentication Flow Differs in Practice

A passkey sign-in uses a key pair. The public key is registered with the service, while the private key stays on the user device or hardware-backed authenticator. During login, the service sends a challenge, and the authenticator signs it after the user approves the request. Because the response is cryptographically bound to the site or app origin, a copied prompt on a fake domain does not produce a valid result.

An OTP flow is simpler but weaker. The service generates a short-lived code and delivers it by SMS, email, or authenticator app. The user copies the code back into the login form, and the service checks whether it matches. That model is better than a permanent password alone, but it still relies on a shared secret that can be exposed in transit, guessed through social engineering, or captured through adversary-in-the-middle phishing.

From a security operations perspective, the practical differences are:

Passkeys reduce replay and relay risk because the challenge response is origin-bound.
OTPs can be intercepted if the delivery channel is compromised or the user is tricked into sharing the code.
Passkeys usually support stronger assurance with less user friction once enrollment is complete.
OTPs are often easier to deploy quickly, but they leave more room for session hijack and real-time phishing.

For organisations, the implementation choice also affects recovery. Passkeys require device and recovery planning, while OTPs require attention to delivery-channel abuse, number portability risk, and email account security. NHI Management Group’s guidance on credential exposure highlights why long-lived or reusable credentials create durable attack paths, and NIST SP 800-53 Rev. 5 remains useful for mapping authentication assurance and access control expectations to a broader program. These controls tend to break down when sign-in is extended to legacy applications that cannot validate origin-bound authentication.

Common Edge Cases and Migration Trade-offs

Tighter sign-in assurance often increases enrollment and recovery complexity, so organisations have to balance phishing resistance against help desk overhead and device lifecycle management. That trade-off is especially visible in mixed environments where some apps support passkeys and others only support OTPs or passwords.

One common edge case is fallback design. If a passkey is deployed but OTP remains a universal fallback, an attacker may simply target the weaker path. Another is account recovery: if recovery still depends on SMS or email, the overall assurance level may be limited by the weakest recovery method rather than the primary sign-in factor.

There is also an important deployment nuance. Passkeys are strongest when they are the primary sign-in method, with policy and recovery designed around them. OTPs can still play a role for transition states, temporary access, or lower-risk scenarios, but current guidance suggests they should not be treated as equivalent to phishing-resistant authentication. For higher-assurance access, the deciding factor is whether the control resists real-time adversary interaction, not whether it simply adds another step.

Risk and Threat Considerations

The main risk difference is exposure to phishing, relay, and account takeover. OTPs are vulnerable because they remain transferable secrets, while passkeys materially reduce the value of a fake login page by binding the response to the legitimate origin and authenticator.

Failure mechanism: OTPs fail when an attacker captures the code in real time through phishing, social engineering, or intermediary relay and immediately reuses it. Passkeys fail far less often in that pattern because the private key never leaves the authenticator and the signed challenge is tied to the genuine service origin.

Impact: With OTPs, a single successful interception can lead to session theft, mailbox compromise, or downstream access to other systems that trust the compromised account. With passkeys, the residual risk shifts toward device compromise, poor recovery design, or fallback paths that still accept weaker authentication.

Standards & Framework Alignment

This section maps relevant standards and security frameworks to the operational risks and controls described in this guidance.

OWASP Non-Human Identity Top 10 and OWASP Agentic AI Top 10 address the attack and risk surface, while NIST CSF 2.0, CIS Controls v8 and NIST Zero Trust (SP 800-207) set the governance and control requirements practitioners need to meet.

Framework	Control / Reference	Relevance
OWASP Non-Human Identity Top 10	NHI-01 — Secrets and Credential Management	Covers credential choice and avoidance of reusable sign-in secrets.
Recommendation — Prefer phishing-resistant credentials and eliminate reusable OTP-style secrets where possible.
NIST CSF 2.0	PR.AC-7 — Users, devices, and services are authenticated commensurate with risk	Addresses stronger authentication assurance for higher-risk sign-in paths.
Recommendation — Apply risk-based authentication and require stronger sign-in for sensitive access.
CIS Controls v8	6.3 — Require MFA for Externally-Exposed Applications	Relevant to protecting exposed sign-in surfaces from account takeover.
Recommendation — Require phishing-resistant MFA for exposed applications and privileged accounts.
NIST Zero Trust (SP 800-207)	3.1 — Policy Engine	Supports real-time, context-aware access decisions for sign-in assurance.
Recommendation — Evaluate authentication context dynamically before granting access.
OWASP Agentic AI Top 10	A2 — Identity and Access	Relevant where autonomous or high-risk workflows depend on secure human sign-in.
Recommendation — Bind high-risk access to stronger identity proofs and reduce fallback weakness.

Practitioner Guidance

Decision rule: If the account protects sensitive data, administrative functions, or high-value workflows, treat passkeys as the preferred primary sign-in method and avoid relying on OTPs as the main assurance factor.

What to verify: Check whether any fallback path still allows SMS, email, or another OTP channel to satisfy the same access decision. If it does, the effective strength of the sign-in flow is closer to the weaker factor than the stronger one.

What practitioners underestimate: The real control question is often recovery, not first login. A strong passkey deployment can still be undermined by weak account reset processes, unmanaged trusted devices, or support workflows that silently reintroduce OTP-style interception risk.

Practitioner takeaway: The best sign-in design is the one that removes the attacker’s ability to reuse what the user just saw, not merely the one that adds a second step.