Installing .MSI and .EXE based applications as part of Autopilot


I am setting up a POC for autopilot for my Azure AD joined devices.


Looking to deploy some applications which are a mix of .MSI and .EXE based ones.


I sure an article from Microsoft that recommends not to mix the above during Autopilot.

Win32 app management in Microsoft Intune | Microsoft Docs

When you're deploying Win32 apps, consider using the Intune Management Extension approach exclusively, particularly when you have a multiple-file Win32 app installer. If you mix the installation of Win32 apps and line-of-business apps during AutoPilot enrollment, the app installation might fail. The Intune management extension is installed automatically when a PowerShell script or Win32 app is assigned to the user or device.


Has anyone ran into problems as mine tests so far have worked.




6 Replies
so far with all the deployments I have done... i did not run into any problems by mixing MSI and win32 applications
best response confirmed by Chris Yue (Contributor)

@Chris Yue 

I would really not recommend to have a mix of MSI (Line-of-business app) and EXE (Windows app (Win32)).
The OMA DM agent can starts an MSI installation and simultaneously the Intune Management Extension plugin can start a Win32 app installation. If your Win32 app would install an MSI as well (embedded), this will cause an issue because it's not possible to have multiple instances of Windows installer (in relation with TrustedInstaller) at the same time.
This is also documented in the following article (See Note):

Mixing MSI and Exe is of course not best practice and not recommended but in many cases, it just works... Just like it's not best practise to push/set required all of your apps during the esp. We try to limit the amount of app required during the esp as possible. ALl other apps which some users need, can be installed manually from the company portal


I'm just speaking about a professional solution/concept, which would never cause any issue. You never know what the future holds...
You could also have this issue outside of the ESP process (meaning when the user is already logged on and has an interactive desktop). In that case, the installation of the impacted apps will be delayed. These apps will be available in worst cases only the next day...

But anyway, these are just recommendations and everyone can do what he wants ;)

So we use a RMM solution called Kaseya VSA. What looks to be the best option in my case is to have Autopilot deploy the VSA agent and nothing more.

Once the agent registers with Kaseya then run a script from Kaseya to deploy the remaining core software instead.

Sometimes you just cant escape from using win32 apps and msi (the intune mgt itself is also installed as msi) . If it was a perfect world.... :)... but i again i totally agree... thats for sure