Microsoft Windows Autopilot streamlines device provisioning through Intune, allowing IT administrators to preconfigure new Windows devices with minimal hands-on effort. However, when combined with Hybrid Entra Join and PKCS certificate deployment, specific challenges arise—particularly with certificate mapping and authentication.

Hybrid Entra Join

During autopilot provisioning, administrators may also choose to join the device to their on-premises Active Directory domain, a deployment model called Hybrid Entra join. Hybrid Entra join presents some unique challenges when using Autopilot to remotely provision devices. Specifically, the user must have connectivity to a domain controller to perform the first logon, as they do not have a user profile on the endpoint.

Device Tunnel

To support offline Hybrid Entra join during Autopilot provisioning, administrators can deploy the Always On VPN device tunnel to provide pre-logon connectivity to domain controllers. A device tunnel connection enables users to log on to their newly provisioned device remotely.

Requirements

The following prerequisites must be met to support the Always On VPN device tunnel.

• The endpoint must be running Windows Enterprise edition.
• An Always On VPN device tunnel profile must be assigned to the device.
• A machine certificate must be deployed to the endpoint that includes the Client Authentication EKU (OID 1.3.6.1.5.5.7.3.2).

Note: If you plan to use the subscription step-up upgrade from Windows Professional to Windows Enterprise, the device tunnel will not connect automatically after provisioning is complete, which prevents the user from logging in. More details and a workaround for this issue can be found here.

Strong Certificate Mapping

Microsoft knowledge base article KB5014754, released in May of 2022, introduced changes to domain controllers to require strong certificate mapping when using certificates to authenticate to Active Directory (AD). It was initially deployed in compatibility mode, only warning administrators when certificates are used for authentication that aren’t strongly mapped. However, full enforcement is mandatory beginning with the September 2025 security updates. This requirement introduces some challenges when issuing certificates to the device using PKCS during Autopilot provisioning.

Intune PKCS Certificates

When using PKCS certificates and the Intune Certificate Connector, the endpoint’s on-premises AD security identifier (SID) is not added to the issued certificate during Autopilot. Interestingly, this does not happen when using SCEP certificates. If the device certificate is not strongly mapped, the Always On VPN device tunnel will still authenticate successfully because Always On VPN does not use AD to authenticate device connections. Instead, Always On VPN simply verifies the certificate (e.g., that it is not expired or revoked) and allows authentication if the certificate passes the validation.

However, enterprise Wi-Fi access may fail without strongly mapped certificates if device authentication is required. Also, there may be other scenarios where a device authentication certificate without strong mapping may cause authentication to fail.

Workarounds

There are a few ways to work around this limitation. Consider the following options.

Native Entra ID Join

The simplest way to avoid the challenges of PKCS certificates and Hybrid Entra join is to avoid it altogether in favor of native Entra join. However, this may not be an option for everyone.

Use SCEP

For some reason, certificates issued with SCEP do not suffer from this limitation. In my testing, SCEP certificates are always strongly mapped. However, deploying SCEP certificates is much more complex than using PKCS. (Pro tip: Cloud PKI for Intune uses SCEP and requires no configuration! It’s definitely something to consider.)

Short-Lived Certificates

Another option is to deploy temporary, short-lived certificates (valid for only a few days) using PKCS to ensure the Always On VPN device tunnel works, and then deploy a permanent, long-term certificate post-deployment that includes the strong mapping. To do this, administrators can leverage dynamic group assignments in Intune. For example, the administrator can assign the short-lived certificate to an Autopilot Provisioning devices group and later assign a long-term certificate to the Hybrid Joined devices group.

Here’s an example of the dynamic group membership configuration.

Autopilot Provisioning Devices:

(device.devicePhysicalIDs -any (_ -contains “[ZTDId]”)) -and (device.deviceTrustType -ne “ServerAD”)

Hybrid Entra Join Devices:

(device.deviceTrustType -eq “ServerAD”)

In this configuration, the initial PKCS certificate is deployed without the strong mapping when the endpoint is enrolled to Autopilot but has not yet joined the domain. During this time, the endpoint will only be a member of the Autopilot Provisioning Devices group and will receive the short-lived, temporary certificate. Later, once the endpoint has successfully joined the domain, the device will move from the provisioning group to the Hybrid Entra Join Devices group. When this happens, a permanent, strongly mapped long-term certificate is enrolled on the device.

Manual Certificate Mapping

Certificates can be manually mapped via the altSecurityIdentities property of the computer object in AD. Obviously, this doesn’t scale well, so my good friend Steve Prentice published a PowerShell script to automate this process. You can find more details and the script here.

Summary

Windows Autopilot streamlines device provisioning with Intune, but Hybrid Entra Join introduces challenges when PKCS certificates lack strong mapping during initial deployment, potentially disrupting VPN and Wi-Fi authentication. Administrators can avoid this by switching to native Entra join or by using workarounds such as switching to SCEP, using short-lived certificates, or manually mapping certificates.

Additional Information

KB5014754 – Certificate-based authentication changes on Windows domain controllers

How To: Map a user to a certificate via all methods available in the altSecurityIdentities attribute

Hybrid Autopilot: Automating altSecurityIdentities

Configure Microsoft Entra hybrid join

Overview: Cloud PKI for Microsoft Intune