Resolving PKCS Certificate Mapping Issues in Windows Autopilot Hybrid Join Deployments

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

Always On VPN and Autopilot Hybrid Azure AD Join

Always On VPN and Autopilot Hybrid Azure AD Join

Windows Autopilot is a cloud-based technology that administrators can use to configure new devices wherever they may be, whether on-premises or in the field. Devices provisioned with Autopilot are Entra ID joined by default and managed using Microsoft Intune. Optionally, an administrator can enable hybrid Entra ID join by also joining the device to an on-premises Active Directory domain using a domain join configuration profile in conjunction with the offline domain-join connector. Although enabling hybrid Entra ID join might sound appealing, there are specific deployment scenarios that present some rather unique and challenging problems when using this option.

Offline Hybrid Entra ID Join

For field-based devices, the device must have connectivity to a domain controller to support the initial login when the user has no local cached credentials. The Always On VPN device tunnel can be deployed in this scenario to provide connectivity and allow the user to log in to a new device the first time without being on-premises. The Always On VPN device tunnel is easily deployed using a Microsoft Intune device configuration policy. Certificates required to support the device tunnel can be deployed with Microsoft Intune and one of the certificate connectors for Intune.

Windows Professional

If a Windows 10 or 11 Professional device is configured using Autopilot, and hybrid Entra ID join is enabled, the Always On VPN device tunnel can still be provisioned, but it won’t start automatically because it requires Enterprise Edition to be fully functional. This prevents the user from being able to logon the first time. The device must be upgraded to Enterprise Edition before the first user logon. There are multiple ways to accomplish this depending on the deployment scenario and activation requirements.

Multiple Activation Key

The easiest way to upgrade Windows 10/11 Professional to Enterprise Edition is to obtain a Multiple Activation Key (MAK) and deploy that to clients using a Microsoft Endpoint Manager configuration profile. Follow the steps below to create a configuration profile to perform this upgrade.

  1. Open the Microsoft Endpoint Manager console and click on Devices > Configuration Profiles.
  2. Click Create profile.
  3. Select Windows 10 and later in the Platform drop-down list.
  4. Select Templates in the Profile type drop-down list.
  5. Select Edition upgrade and mode switch from the list of templates.
  6. Click Create.

Use the following steps to configure the settings for the configuration profile.

  1. Enter a descriptive name for the configuration profile in the Name field.
  2. Enter a description for the profile in the Description field (optional).
  3. Click Next.
  4. Expand the Edition Upgrade section and select Windows 10 Enterprise from the Edition to upgrade to drop-down list.
  5. Enter your multiple activation product key in the Product Key field.

    Always On VPN and Autopilot Hybrid Azure AD Join

Once complete, assign the configuration profile to the appropriate groups and click Create.

KMS Activation

If Key Management Service (KMS) activation is required, follow the steps listed previously for MAK. Enter the KMS client setup key for Windows 10/11 Enterprise which is NPPR9-FWDCX-D2C8J-H872K-2YT43. The device will complete KMS activation when it can connect to the on-premises KMS host.

Subscription Activation

Windows 10/11 Enterprise Edition licensing is included in some Microsoft 365 subscriptions. This poses a unique challenge for hybrid Azure AD join scenarios, however. Specifically, subscription activation is a “step-up” process that requires Windows 10 Professional to have been successfully activated previously. Also, this occurs after the user logs on, but the user cannot log on unless the device tunnel is active. Catch 22!

Workaround

A multi-step process is required to address the limitations imposed by subscription activation. To begin, the device must be upgraded to Enterprise Edition, so the device tunnel is available for the initial user logon. This is a temporary, one-time upgrade to Enterprise Edition solely for the purpose of getting the device tunnel to connect and allow the user to authenticate.

To begin, download this PowerShell script and follow the steps below to deploy it to Windows 10 devices using Microsoft Endpoint Manager.

  1. Open the Microsoft Endpoint Manager console and click on Devices > Scripts.
  2. Click Add and select Windows 10.
  3. Enter a descriptive name for the configuration profile in the Name field.
  4. Enter a description for the profile in the Description field (optional).
  5. Click Next.
  6. Enter the location of the PowerShell script in the Script location field.
  7. Click Next, then assign the script to the appropriate device group(s) and click Add.

The PowerShell script will automatically install the KMS client setup key for Windows 10 Enterprise Edition, then restart the network interfaces to ensure the device tunnel starts. This will immediately upgrade the client device to Windows Enterprise Edition and allow the user to authenticate.

Subscription activation with a step-up upgrade to Enterprise Edition still requires that Windows Professional be activated first. To accomplish this, the embedded Windows Professional key must be re-installed on the client. To do this, download this PowerShell script and follow the same steps listed previously to deploy a PowerShell script with Microsoft Endpoint Manager. However, this script should be assigned to users, not devices.

Once this script is run on the client it will be downgraded (temporarily) to Windows Professional edition. After activation is successful, subscription activation will once again upgrade the client to Windows Enterprise Edition.

Considerations

As you can see, the process of getting a Windows Professional edition client onboarded in a hybrid Entra ID joined scenario is somewhat complex. My advice is to avoid this scenario whenever possible. Access to on-premises resources with the Always On VPN user tunnel with full single sign-on support is still available for users on Windows 10/11 devices that are Entra ID joined only. Unless there is a specific requirement to manage client devices using on-premises Active Directory and group policy, consider choosing native Entra ID join with Autopilot and manage devices using Microsoft Intune exclusively.

Special Thanks

I would like to extend a special thank you to everyone in the Microsoft Intune community who provided valuable input and feedback for me on this topic, especially John Marcum, Michael Niehaus, and Sandy Zeng. Follow the #MsIntune hashtag on X to keep up on all things Microsoft Endpoint Manager.

Additional Information

Overview of Windows Autopilot

Windows 10 Subscription Activation

Windows 10 Always On VPN Class-Based Default Route and Microsoft Endpoint Manager

Windows 10 Always On VPN Device Tunnel and Custom Cryptography in Microsoft Endpoint Manager