Passwords are a single point of failure. Adding multi-factor authentication (MFA) reduces account compromise risk by requiring a second, independent proof of identity, something you have or something you are, in addition to something you know.
For Active Directory environments, this means protecting privileged accounts, remote access, and hybrid cloud sign-ins with a second factor and applying conditional access for higher-risk scenarios.
Security and IT teams should follow NIST guidance and Microsoft’s recommended flows for Entra ID and ADFS when setting up MFA.
How to Enable Multi-Factor Authentication for Active Directory
Enabling MFA in Active Directory is a structured rollout that touches identity flows, policies, legacy integrations, and user behavior. The right setup depends on whether you’re cloud-first, hybrid, or strictly on-prem. Below is a practical, step-by-step breakdown to help you implement MFA securely, test it properly, and avoid locking out half your workforce on day one
1. Plan and prepare
- Inventory privileged, service, and remote-access accounts.
- Choose allowed factors. Prefer phishing-resistant options (authenticator apps, hardware FIDO2 keys). Avoid SMS/email for high-risk accounts where possible.
- Select a pilot group (admins + remote users), build user guides, and prepare helpdesk runbooks for lost devices and emergency access.
2. Microsoft Entra ID MFA (cloud or hybrid)
- Create a pilot group and enable Microsoft Entra ID MFA for that group.
- Use Conditional Access policies to require MFA for privileged roles, risky sign-ins, or critical apps.
- Configure allowed authentication methods (Authenticator app, OATH tokens, FIDO2).
- Test user registration, SSO behavior for hybrid/joined devices, and application access before broad rollout. Microsoft documents the Entra MFA and Conditional Access setup steps.
3. AD FS on-prem MFA (if you must keep auth local)
- Install and configure the AD FS role. Add the MFA provider. For Microsoft Entra MFA integration you’ll generate and install the tenant certificate on each AD FS server and register the MFA adapter.
- Update global or relying-party access control policies to require extra authentication for selected apps or groups.
- Test with pilot users, verify certificate renewal and AD FS farm consistency, and document failover behavior. Microsoft provides step-by-step guidance for AD FS + Entra MFA.
4. Third-party MFA integration
Many organizations use a third-party MFA provider to get specific factors, device management, or advanced policy controls. Typical integration patterns with Active Directory are: RADIUS (NPS), AD FS adapter, or an identity bridge/agent that syncs with AD. Here’s a practical sequence.Many organizations use a third-party MFA provider to get specific factors, device management, or advanced policy controls. Typical integration patterns with Active Directory are: RADIUS (NPS), AD FS adapter, or an identity bridge/agent that syncs with AD. Here’s a practical sequence.
- Choose a vendor that supports the factors and workflows you need (see vendor list below). Verify AD integration options (AD agent, LDAP, RADIUS, AD FS adapter).
- Deploy the vendor’s AD connector or agent. This usually runs on a domain-joined server and synchronizes users/groups or proxies authentication to AD. Follow vendor agent hardening guidance.
- If using RADIUS. Configure Microsoft NPS (Network Policy Server) or the vendor’s RADIUS proxy. Point services (VPN, Wi-Fi controllers) to the RADIUS endpoint so primary auth goes to AD and the vendor performs the second factor. Microsoft docs cover NPS / RADIUS architecture.
- If using AD FS. Install the vendor’s AD FS MFA adapter on each AD FS instance in the farm. Configure the adapter and enable it in AD FS Authentication Policies. Test certs, high availability, and adapter failover behavior.
- Configure user enrollment and recovery workflows. Provide self-service registration, backup methods (hardware token or recovery codes), and helpdesk processes for factor reset. Monitor logs for failed or bypassed MFA events.
5. Operationalize and monitor
- Publish user how-to guides and run helpdesk training.
- Keep at least two break-glass emergency accounts with strict controls for disaster recovery.
- Enable logging and alerts for failed MFA attempts, suspicious bypass events, and anomalous sign-ins; archive logs for audits. OWASP advises strong logging and protective controls around MFA flows.
Which Approach Fits Your Environment? Microsoft Entra ID vs AD FS vs Third-Parties
Microsoft Entra MFA: Best fit for cloud-first or hybrid organizations. Tight integration with Conditional Access, risk signals, and modern authentication methods makes Entra the simplest managed option for broad MFA coverage.
AD FS + MFA adapters: Use when authentication must stay on-prem, or legacy apps require AD FS. Offers control but costs more in operations: certificate management, adapter installation across the farm, and high availability.
Third-party MFA solutions: Use when you need specific hardware key support, advanced device posture checks, or a vendor-centric admin experience. They commonly integrate via AD agent, RADIUS/NPS, or AD FS adapters. Evaluate cost, vendor SLAs, phishing resistance, and compliance support.You can consider using few representative third-party tools, including Cisco Duo, Okta Adaptive MFA, OneLogin, etc.
Conclusion
Multi-factor authentication is a baseline security control for Active Directory, not an advanced add-on. Whether you use Microsoft Entra, AD FS, or a third-party provider, the objective is simple: stop credential-based attacks without disrupting users.
Start with privileged and remote access accounts, choose strong, phishing-resistant factors, and roll out MFA in controlled phases. Just as important, monitor authentication activity and policy changes continuously. MFA only works when it’s enforced consistently, reviewed regularly, and backed by visibility into who’s accessing what and ho
