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Delete A Cloud PKI for Intune Certificate Authority

When Microsoft first introduced Cloud PKI for Intune, the solution did not allow administrators to delete a CA after it was created. As you are limited to just six Cloud PKI for Intune CAs, this was quite frustrating, especially during the testing and evaluation phase, where you may need to spin up a few instances before you decide on the features you need.

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Delete Cloud PKI

Thankfully, Microsoft eventually realized this shortcoming and added this much needed feature a few months ago. However, removing an Intune Cloud PKI CA requires administrators to follow some specific steps to remove a CA successfully. Since Cloud PKI for Intune uses a two-tier deployment model, administrators must remove the issuing CA first and then the root CA if required.

Issuing CA

Follow the steps below to delete a Cloud PKI for Intune issuing CA.

Intune Policies

Be sure to delete any Intune device configuration policies relating to Cloud PKI for Intune before decommissioning a Cloud PKI for Intune CA. This includes trusted certificate policies, Wi-Fi policies, and VPN policies.

Pause CA

The first step of deleting a Cloud PKI for Intune CA is to pause the service. Pausing the service prevents new certificates from being issued while the administrator completes the remaining retirement tasks. Open the Intune portal (https://intune.microsoft.com), navigate to Tenant Administration > Cloud PKI, and click the CA to be deleted. Next, click Pause to pause the CA.

Revoke Certificates

Administrators must revoke all issued certificates before deleting the issuing CA. Click on any issued certificate to view its properties and then click the Revoke button, as shown here.

Complete this step for each certificate issued and active on the CA.

Note: It takes some time before the certificate status shows Revoked in the management console. Be patient!

Revoke CA Certificate

Once the administrator has revoked all issued certificates, click Revoke to revoke the issuing CA’s certificate.

Delete CA

Once the issuing CA certificate has been revoked the administrator will now have the option to delete the Cloud PKI for Intune issuing CA.

Root CA

After the administrator deletes the issuing CA, the root CA can be removed if necessary. Click on the root CA and click the Delete button.

Additional Information

Delete Microsoft Cloud PKI Certification Authority

Strong Certificate Mapping for Intune PKCS and SCEP Certificates

Microsoft Cloud PKI for Intune and Certificate Templates

Microsoft Cloud PKI for Intune and Active Directory

Microsoft Cloud PKI for Intune SCEP URL

Microsoft Cloud PKI for Intune on RunAs Radio

Microsoft Intune Certificate Connector Failure

The Microsoft Intune Certificate Connector enables the provisioning and de-provisioning of on-premises PKI certificates for Intune-managed devices. Always On VPN administrators using Intune to deploy certificates with the Intune Certificate Connector using either PKCS or SCEP may encounter a scenario where certificates are no longer being provisioned to users or devices after working reliably previously.

Certificate Not Found

When this issue occurs, users will no longer be able to access the VPN and receive a “certificate could not be found that can be used with this Extensible Authentication Protocol” error message.

Connector Status

To determine the status of the Intune Certificate Connector, open the Microsoft Intune Admin Center (https://intune.microsoft.com) and navigate to Tenant Administration > Connectors and Tokens > Certificate Connectors. The status of the certificate connector server will be in Error.

Event Log

Open the event log on the server where the Intune Certificate Connector is installed. Navigate to Applications and Services Logs > Microsoft > Intune > CertificateConnectors > Operational. Here, you will find a variety of warning and error messages.

Event ID 5001

This is a warning from the CertificateConnectors source with event ID 5001 in the Task Category HealthMessageUploadFailedAttempt with the following details.

PKI Create Service:

Failed to upload health messages. Requeuing messages.

Event ID 1003

This is an error from the CertificateConnectors source with event ID 1003 in the Task Category PkcsDownloadFailure with the following details.

PKI Create Service:

Failed to download PKCS requests.

Event ID 2

This is an error from the CertificateConnectors source with event ID 2 in the Task Category Exception with the following details.

PKI Create Service:

Microsoft.Intune.Connectors.PkiCreateProcessor.Process threw an exception.

Expired Certificate

The warning and error messages recorded in the event log indicate an expired certificate on the Intune Certificate Connector server. Open the local computer certificate store (certlm.msc) on the server where the Intune Certificate Connector is installed. Review the expiration date of the certificate issued by Microsoft Intune ImportPFX Connector CA. It is most likely expired.

Click on the Certification Path tab to view the certificate status.

Renew Certificate

To renew this certificate, you must reinstall the Intune Certificate Connector. However, you do not have to uninstall it first. To renew the certificate, navigate to C:\Program Files\Microsoft Intune\PFXCertificateConnector\ConnectorUI and double-click on PFXCertificateConnectorUI.exe. Follow the prompts without making changes to the existing configuration. You’ll be prompted for the service account password (if using a domain account) and proxy credentials (if using a proxy server). In addition, you’ll be asked to sign in to Entra ID (formerly Azure AD). Be sure to provide credentials that are a global administrator and have an Intune license assigned. Once the process is complete, a new certificate will be installed in the local computer certificate store.

Intune Configuration

After updating the Intune Certificate Connector, a new certificate connector appears in the Intune Admin Center. You can now safely delete the old connector and rename the new one accordingly.

Redundancy

Deploying multiple instances of the Intune Certificate Connector is an excellent way to avoid future outages! It’s also a good idea to stagger their installation by a few months to ensure that a future certificate expiration doesn’t result in lost functionality. If you’ve deployed Intune Certificate Connectors recently, consider updating them at rotating intervals so certificates expire at different times.