Using a custom certificate store for Configuration Manager client authentication certificates

Author: Ray Rosen, Microsoft Premier Field Engineering

Public Key Infrastructure (PKI) is used in varying degrees in different organizations, and since System Center Configuration Manager 2007, it has been leveraged to support Internet Based Client Management. PKI is also an option to identify systems, as the Discovery Data Manager automatically approves clients when a PKI certificate is used for client identity. As long as the site systems that handle client communication trust the client authentication certificate chain, then the client receives service.

When an organization stands up PKI simply to support Configuration Manager, no contention exists within the computer’s certificate personal store. This is the default location where a new certificate is installed for the computer. However, when an organization heavily leverages PKI, the default personal store may contain a number of certificates, and the situation may complicate the usage of certificates for Line of Business (LOB) applications, Configuration Manager, or both.

Configuration manager allows the administrator to specify strings or attributes in the certificate subject or subject alternative name to select a certificate, but when the Configuration Manager client certificate’s presence in the personal store affects a LOB application, the fact that Configuration Manager is ‘OK’ provides little relief to the administrator. To better handle the scenario, the admin may instead specify a custom certificate store for selecting a client authentication certificate, which eliminates any conflict with other applications. Here’s an example of how to leverage this capability.

First we need a certificate template to issue certificates for client authentication. Use the same process as always to duplicate the Workstation Authentication template for this purpose and give the template a meaningful name, but do not enable Autoenrollment.


Note that Template name will omit spaces that exist in Template display name. Also set the security on the template for Domain Computers and Domain Controllers to Read and Enroll the certificate. Autoenroll is not required since we will use a script to issue the certificate.


Once the template is created, instruct the Certificate Authority to issue the certificate. When complete, it will appear in the main Certificates Templates screen:


Next, a script needs to run on each client to perform the following:

  1. Create a custom certificate store if one does not exist.
  2. Request a new certificate if one does not exist in the custom store.
  3. Request a new certificate if all existing certificates are about to expire in the custom store.

So why use a script instead of Autoenroll? The goal is to avoid contention in the personal store, and the fastest way to ensure a clean personal store is to move the certificate out of the personal store immediately after it is installed. This option does not exist for Autoenrollment.

A sample script to do this is posted here, however please note that this script will only work on Windows 8 and Windows Server 2012 or later. The script needs to run as local system or administrator on every client, and depending on the environment, this can be accomplished by one of the following:

  1. Using a startup script via GPO
  2. Setting up a Task Scheduler task to call it from a network share via GPO
  3. If already a Configuration Manger client and a HTTP MP will persist, a Compliance Settings script, package deployment, etc. could do the job.

Whichever method you choose, the script needs to run at least as frequently as the number of days specified before expiration so you can ensure that a new certificate always replaces an expiring one before it expires.

After the script has executed, the site properties can be modified to use the custom store as specified in your script:


On the next machine policy poll after committing the site properties change, the clients will use the new settings and look for a client authentication certificate in the custom store. Once found, it will be used to update the client’s registration with its primary site and become the client’s new crypto identity.

Ray Rosen, Microsoft Premier Field Engineering

Comments (5)
  1. Frank says:

    Hi Ray,
    Will the client fall back to the default personal store when there is a custom store specified in ConfigMgr but there is not yet a custom store or the custom tore is empty. But there is a valid certificate in the default personal store?

    1. Ray Rosen says:

      Hi Frank,

      No, the setting will only allow the client to use the custom store when one is specified.

  2. Oliver says:


    how does this work in a OSD Scenario with https only configuration ?


    1. Ray Rosen says:

      Hi Oliver,

      Good question. During OSD a non-client specific certificate is used. Once the TS completes, the client will need to register with its own certificate outside of provisioning mode. Therefore, running a script in full Windows after domain join should do the trick in populating the certificate. I have not tested this scenario.

  3. John says:

    Considering the large numbers of companies that are still on Windows 7 (including mine), does anyone know what tools we could use to script this for that OS?

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