Henk’s blog: Issue in ConfigMgr Current Branch (1602) with Intune subscription

Part 2 – deploying microsoft intune connector in an enterprise world: troubleshooting

In a diptych I’m sharing my experiences, common practices and challenges of implementing Microsoft Intune PFX connector as certificate deployment mechanism in the enterprise.


In my first blog post I covered the basics of implementing a certificate deployment infrastructure based on Microsoft Intune PFX connector. Explained the differences and considerations whether to choose SCEP or PFX as your certificate deployment solution. And explained the certificate issuing workflow. In this second post I’ll go in more detail of the anatomy of the Intune Certificate Connector, setup. Explaining the renewal and revocation process(flow) works. And lastly I give you some pointers where to start your journey, in case of troubleshooting certificate deployment issues.

Part 1 – Deploying Microsoft Intune Connector in an Enterprise world: common practices

Part 2 – Deploying Microsoft Intune Connector in an Enterprise world: troubleshooting


The Intune Certificate Connector forms the connection between your on-premise certificate (CA) infrastructure and Microsoft Intune cloud services in order to issue certificates to you managed endpoints. The Intune Certificate Connector can be downloaded once you enabled the Certificate Connector in your Intune subscription.

During the setup of the Intune Certificate Connector you’ve the option to configure SCEP and PFX of PFX only.


Service Account

By default the Windows service of the Intune Certificate Connector runs under the computer account security context of where the Intune Certificate Connector is installed on. Make sure when specified a service account, it has Issue and Manage Certificates permission on your issuing Certificate Authority (specifying a service account is optional).

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Once you installed and successfully registered the Intune Certificate Connector the connection status appears Active in you Intune subscription. From here you’ll deploy a trusted root and intermediate (if applicable) followed by a PFX certificate profile. In the table below all components shown of which the Intune Certificate Connector consists of.


Troubleshooting Intune Certificate Connector can be challenging. Understanding the process and autonomy gives you a good starting point to successfully determine the issue or even solve your problem. In the table below most common steps involved are listed in chronological order.

WCF Trace Viewer

The log files of the Intune Certificate Connector are generated in a *.svclog file extension. Best way to analyze these log files in a readable format is Windows Trace viewer. Windows Communication Foundation (WCF) Service Trace Viewer Tool helps you analyze diagnostic traces that are generated by WCF. Service Trace Viewer provides a way to easily merge, view, and filter trace messages in the log so that you can diagnose, repair, and verify WCF service issues.




The Intune Certificate Connector is frequently updated and includes often fixes or (service) improvements. Unfortunately both Silverlight- and new Azure Intune portal doesn’t provide insights (yet) whether you’ve installed the latest version of the connector.

When you’re planning to update the connector than it’s good to know there is no impact other than the Intune Certificate Connector services will be restarted during the upgrade. There is no need to provide your Intune Service admin or Global admin credentials. The service credentials (certificate) remains preserved.

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In case you’ve to re-register the Intune Certificate Connector you must delete SC_Online_Issuing certificate(s) (Local Computer)PersonalCertificates) prior to re-register the Intune Certificate Connector. Re-registering might be required as part of a fallback scenario as described in my first blog. Re-registering doesn’t require you to reinstall the Intune Certificate Connector. The re-registration is initiated by starting the Intune Certificate Connector UI.

Advanced Troubleshooting

When the default log files are insufficient, the log level (debug/verbose) can be configured by adjusting the NDESConnector.exe.config. Besides log levels, we can adjusts the TimeFrequency, PFXTimeFrequency and IntuneServiceTimeout.


Be reluctant on changing your certificate parameters in your certificate policies. Changing one of these parameters will cause reissuing of all certificates! This impacts the user(s) of which the certificate policy were targeted to.


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