How to Solve Common Certificate-Based Wi-Fi Authentication Issues in Intune

Certificate-based authentication has become the industry standard for securing Wi-Fi networks, especially with organizations moving toward stronger security and passwordless authentication. Microsoft Intune is one of the most widely used MDM platforms for deploying and managing device certificates. Organizations can often encounter several issues when setting up certificate-based Wi-Fi authentication.

Certificates provide a secure, passwordless authentication method, but configuring them correctly across devices, RADIUS, and the Certificate Authority (CA) can be tricky. Misconfigurations can cause enrollment failures, failed connections, or policy mismatches that lead to frustrating end-user experiences and network downtime.

In this blog, we’ll cover IT teams’ most common issues, their causes, and fixes with certificate-based Wi-Fi authentication in Intune.

Certificates Not Delivered

One of the most common issues is when devices fail to get a certificate from the CA, leaving them unable to authenticate.

Cause #1: Misconfigured Intune SCEP or PKCS profile

Fix: Double-check that the SCEP/PKCS profile is configured correctly in Intune and assigned to the right user/device groups. Also, verify that the certificate template’s Key Usage (KU) and Enhanced Key Usage (EKU) are aligned, and the certificates must include Client Authentication EKU to be valid for RADIUS authentication.

Cause #2: Incorrect NDES connector configuration

Fix: Validate that the NDES connector is installed, running, and synced with Azure AD. Review event logs for enrollment errors to identify any misconfigurations.

Cause #3: Missing permissions for the Intune Connector to enroll certificates on behalf of users/devices

Fix: Ensure the ADCS certificate template allows enrollment from the NDES/Intune connector.

Cause #4: Device not compliant with Conditional Access or Intune compliance policies

Fix: Verify that devices meet Intune and Conditional Access requirements (e.g., up-to-date OS, not jailbroken). Devices blocked by Conditional Access will fail certificate delivery, even if all other configurations are correct.

Cause #5: Intune Management Extension not installed or functioning properly

Fix: Confirm the Intune Management Extension is present and running on the device, as it handles profile and certificate deployment on Windows endpoints.

Cause #6: Failure point unclear (Intune vs connector side)

Fix: Use Intune MDM logs (MDM Diagnostic Tool for Windows or Company Portal logs for iOS/Android) to confirm whether the request fails at the Intune or the connector side.

Wi-Fi Profile Misconfiguration in Intune

Sometimes the issue is not the certificate, but the Wi-Fi profile. In this case, the devices receive a certificate but fail to connect to Wi-Fi because Intune’s Wi-Fi profile is incorrectly configured.

Cause #1: Incorrect SSID (case-sensitive)

Fix: Ensure the SSID matches the configuration of the enterprise SSID (case-sensitive).

Cause #2: Wrong EAP type selected (PEAP/MS-CHAPv2).

Fix: Set the EAP type to EAP-TLS.

Cause #3: Trusted Root CA not delivered to devices.

Fix: Push the Trusted Root CA certificate profile via Intune so they can trust the issuing CA of the server certificate used by the RADIUS.

Cause #4: Authentication mode misconfigured (user vs. device).

Fix: Use device authentication to deploy computer certificates, or user authentication to deploy user certificates.

Cause #5: Profiles assigned to the wrong device/user group, or sequencing issues between Wi-Fi and certificate deployment.

Fix: Assign Wi-Fi and certificate profiles to the same Azure AD group to ensure proper sequencing.

Cause #6: OS-specific payload requirements and MDM platform limitations (Android/iOS differences with PKCS vs. SCEP).

Fix: Different platforms require tailored certificate profiles to work correctly. iOS and macOS devices need PKCS payloads with proper keychain settings, Android devices require SCEP profiles with challenge passwords, and Windows devices support standard PKCS or SCEP profiles as long as device enrollment is compatible. Always validate each platform’s payload requirements in Intune to prevent deployment failures.

RADIUS Authentication Failures

Even if certificates are installed on devices, authentication will fail if the RADIUS server isn’t configured to verify those certificates properly.

Cause #1: RADIUS is not configured to trust the issuing CA.

Fix: Import the Root and Intermediate CA certificates into the RADIUS server’s trusted certificate store.

Cause #2: Intermediate certificates are missing on the RADIUS server.

Fix: Confirm that all intermediate certificates are installed and chained properly in the RADIUS server’s certificate store.

Cause #3: Wrong server certificate selected for NPS (or missing EKU).

Fix: In Network Policy Server (NPS), configure the network policy to support EAP-TLS, select the correct server certificate, and verify the EKU is valid for server authentication.

Cause #4: Policy mismatch between RADIUS and certificate attributes (e.g., EKU, SAN, or Subject Name misaligned).

Fix: Check the certificate attributes (Subject Name, SAN, EKU), and ensure they align with the RADIUS policies (e.g., SAN contains UPN for user authentication, or device hostname for machine authentication).

Cause #5: Certificate expired, invalid, or CRL/OCSP issues.

Fix: Use RADIUS debug logs (e.g., nps.mdb or IAS.log) to verify certificate validity, confirm CRL/OCSP accessibility, and reissue/renew certificates as needed.

Certificate Expiration and Renewal Issues

Authentication may work during the initial rollout, but may break later when certificates expire because renewal policies were not correctly configured.

Cause #1: Certificates issued with short lifetimes and no auto-renewal configured.

Fix: Configure certificate lifetimes in Intune (e.g., 1 year) and enable auto-renewal, ensuring devices renew at around 80% of the certificate’s lifetime. Also, confirm that the certificate’s Key Usage (KU) and Extended Key Usage (EKU) align with renewal requirements, as misalignment can prevent successful auto-renewal.

Cause #2: The device did not contact Intune/MDM in time for renewal.

Fix: Ensure devices check in regularly with Intune. Renewal timing differs based on join type: Hybrid Azure AD-joined devices follow on-premises AD renewal schedules, while Azure AD-joined devices rely on MDM check-ins. For Windows, run certutil –pulse, and for mobile, confirm MDM renewal policies. Troubleshoot if certain OS platforms stop syncing.

Cause #3: Intune Connector unable to reach the CA for renewal requests.

Fix: Verify network connectivity and permissions for the Intune Connector to communicate with the CA.

Cause #4: Expired root or intermediate CA certificates not replaced.

Fix: Rotate and update root/intermediate CA certificates across endpoints and RADIUS servers before expiry.

Cause #5: Lack of visibility into upcoming certificate expirations.

Fix: Use Intune’s built-in compliance policies and alerting dashboards to monitor certificate lifetimes, and consider integrating third-party monitoring tools to notify admins before certificates expire.

Multi-Platform Compatibility Challenges

Managing certificates across different devices and OS (Windows, iOS, macOS, and Android) can be tricky. Each platform has unique requirements, which can lead to deployment issues if not handled carefully.

Cause #1: iOS/macOS require different certificate payloads than Windows/Android.

Fix: iOS and macOS require client certificates to be installed in the correct keychain and properly associated for TLS identity selection. On Android, SCEP vs. PKCS payloads may differ depending on the OS version. To avoid authentication failures, create platform-specific certificate profiles in Intune for Windows, iOS, macOS, and Android.

Cause #2: Keychain storage issues on Apple devices.

Fix: Test certificate profiles thoroughly on Apple devices and validate storage behavior before deployment.

Cause #3: Legacy devices may not support newer cryptographic algorithms.

Fix: Use modern cryptographic standards (RSA 2048+, SHA-256) but confirm compatibility across all client devices.

Cause #4: BYOD and work profile devices complicate secure certificate enrollment.

Fix: For Android Work Profile devices, ensure certificates are installed in the work profile to avoid authentication issues. On iOS BYOD/unmanaged devices, use SCEP with challenge passwords to securely enroll certificates.

Troubleshooting Tips for Intune Certificate Authentication

• Use the Test Connectivity option in Intune Wi-Fi profiles.
• Run netsh wlan show wlanreport on Windows devices to gather detailed Wi-Fi authentication logs.
• For iOS/Android, export device logs from the Company Portal and review them for MDM payload errors.
• Always check time synchronization between client devices, RADIUS servers, and CAs – mismatched time is a common root cause for TLS failures.

Why Cloud RADIUS Solves These Issues

While Intune does a good job of distributing certificates, the real complexity lies in managing RADIUS authentication. Traditional RADIUS servers like NPS are rigid, require on-premises maintenance, and don’t integrate easily with cloud identity providers.

SecureW2’s Cloud RADIUS solves these challenges by:

1. Natively integrating with Intune for certificate distribution.
2. Eliminating passwords with modern protocols like EAP-TLS without requiring on-prem NPS or complex AD integrations.
3. Automatically updating trusted roots and intermediates
4. Delivering global high availability that on-prem servers can’t match.

Intune Wi-Fi Certificate Authentication: On-Prem vs Cloud RADIUS

Feature	Intune + NPS (On-Prem)	Intune + Cloud RADIUS
Deployment Effort	High (NDES, PKI, connectors, firewalls)	Low (cloud-native integration)
Scalability	Limited by hardware	Elastic, cloud-scale
Certificate Trust	Manual updates required	Automated trust propagation
Policy Enforcement	Basic AD mapping	Advanced, contextual
Availability	Single point of failure	Redundant, geo-distributed
Maintenance	Ongoing patching, cert updates	Managed by the provider

Final Words

Certificate-based Wi-Fi authentication in Intune is one of the most secure methods to protect enterprise networks, but the technical complexity often leads to several challenges. By understanding the common issues and the causes behind them, you can methodically troubleshoot and resolve problems.

For organizations looking to avoid these challenges, SecureW2’s Cloud RADIUS and PKI solutions provide a streamlined, passwordless approach that integrates effortlessly with Intune and Azure AD, ensuring a secure, scalable, and future-proof authentication infrastructure.

Contact us now to see how SecureW2 can help eliminate the issues, secure your Wi-Fi, and ensure seamless access for all users.