In-Depth Guide to Microsoft Entra Certificate-Based Authentication (CBA)

What is Certificate-Based Authentication (CBA)?

Certificate-Based Authentication (CBA) is a passwordless authentication mechanism that relies on digital certificates issued by a trusted Certificate Authority (CA). It replaces traditional passwords with cryptographic keys to verify the identity of users, devices, or services.

💡 How It Works:

A digital certificate contains information such as a public key, subject name (user/device info), serial number, issuer info, and more.
The certificate is installed on the client device (or stored in a smartcard, USB key, or TPM).
When a user attempts to authenticate, the system challenges the certificate.
The user proves possession of the private key associated with the certificate.
The authentication server validates the certificate against the trusted CA chain and checks for revocation.

This ensures the entity presenting the certificate is legitimate.

Microsoft Entra and CBA

Microsoft Entra ID (formerly Azure Active Directory) supports CBA for both cloud-native and hybrid identities. It allows users to sign in to:

Web applications (e.g., Microsoft 365)
Entra-joined or hybrid-joined devices
Conditional Access-enabled services

📈 Why Use CBA?
Benefit	Description
🛡️ Phishing Resistant	Private keys are never shared and certificates can’t be socially engineered like passwords.
💼 Enterprise-Grade Security	Supports strict compliance needs like those in finance, defense, and healthcare.
🔐 Passwordless Experience	Users only need to insert a smartcard or token, select a certificate, and enter a PIN.
🧰 No On-Prem Required	Cloud-native configuration using Microsoft Entra Admin Center — no need for ADFS or on-prem servers.
🔄 Support for SSO & MFA	CBA integrates with Microsoft Conditional Access and MFA policies.
🌍 Device & Endpoint Compatibility	Works on Windows, macOS, iOS, Android, smartcards, YubiKeys, and virtual smartcards.

Step-by-Step CBA Configuration in Microsoft Entra

🔧 Pre-requisites

Trusted CA(s) issuing certificates
Certificate templates with subject/issuer info
CRL or OCSP endpoint (for revocation)
Group of users for testing

Step 1: Upload Certificate Authorities

📍Where:
Entra Admin Center → Protection → Security Center → Certificate Authorities

📄 What You Upload:

Root CA: The top-most authority in the chain
Intermediate CA(s): Subordinate authorities issuing certificates

🛑 Important Configuration:

Configure the Certificate Revocation List (CRL) or OCSP.
Without this, revoked certificates will still be accepted, posing a major risk.

💡 Tip: Use Base64 PEM format when uploading.

Step 2: Enable CBA in Authentication Methods

📍Where:
Entra Admin Center → Authentication Methods → Certificate-Based Authentication

📌 Configuration Options:

Targeting: Choose either “All users” or a specific group.
- Best practice: Use a test group first.
Protection Level:
- 🔐 Single Factor: Cert only.
- 🔐 Multi-Factor: Certificate protected with biometric or PIN.
Default Binding Strengths:
- Can be overridden using custom rules based on Policy OID, Issuer, or Certificate Field.

Step 3: Authentication Binding

Authentication binding defines the strength of the authentication method used.

🟡 Low Affinity Binding:

Uses certificate fields like:
- Subject Alternative Name (SAN)
- RFC822 Name
- Principal Name (UPN)
These can be reused and don’t change on certificate rotation.

🟢 High Affinity Binding:

Uses fields like:
- Subject Key Identifier (SKI)
- Serial Number
These are unique and regenerate with every certificate issuance.

📊 Security Tip: Always prefer high-affinity bindings for multi-factor scenarios.

Step 4: Create Custom Rules

You can apply custom logic using:

Certificate Issuer
Policy Object Identifier (OID)
Authentication Strength override
Binding Strength override

💡Example:
If Policy OID = 1.2.840.113549.1.9.1, treat it as multi-factor because it was issued to smartcards with biometrics.

Step 5: Configure Username Binding

Username Binding maps a certificate field value to a user attribute in Entra ID.

🔁 Examples:

Map SAN.UPN → userPrincipalName
Map SKI → extensionAttribute1

💡 Ensure that the mapped value exists on the user object; otherwise, authentication will fail.

Step 6: Add SKI to User Profile

If you’re using Subject Key Identifier (SKI) for authentication:

Locate the certificate.
Copy the SKI.
Paste it into the corresponding user attribute in Entra.
Save changes.

This ensures Entra can map the certificate to the user correctly.

Testing & Validation

Use Test Users in your CBA-enabled group.
Monitor sign-in logs in Microsoft Entra Admin Center.
Validate:
- Certificate validity and CRL checks
- Username bindings
- Authentication method strength

Final Thoughts

Microsoft Entra Certificate-Based Authentication delivers a modern, secure, and scalable approach to passwordless identity management. Whether you’re building a Zero Trust architecture, migrating from on-prem solutions, or hardening your user login process, CBA can significantly enhance your security and compliance posture.