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  • Writer's pictureGareth Oxendine

Updating Windows Applications using Intune

Updating applications deployed to your machines plays a crucial part in managing endpoints. Why update applications? See below:

  • to fix bugs

  • to patch security flaws

  • as preventative maintenance

  • so new machines receive the "latest and greatest"


Software on end users' machines was installed in one of three ways. Either the software was deployed using Intune, the end-user installed it independently, or it came preinstalled on the computer. The steps provided below address all of the scenarios.


Table of Contents


Updating MSI (Line of Business) Applications

Option 1: Use Intune and a Line of Business App

Whether the original (outdated) application was deployed with Intune or not, you can use this option to deploy the new version. Most likely, the new installer file will automatically update the outdated version already installed on the end users' machines.


Step 1: Inspect the New MSI File

Remember that MSI files have a property called the UpgradeCode. If the new MSI has the same UpgradeCode value as the original MSI, then Intune will treat these as the same application but as different versions. You may not have the original MSI file if you did not originally deploy the application with Intune.


Using Orca to view the UpgradeCode of an MSI file.
Using Orca to view the UpgradeCode of an MSI file.

Sometimes the application's vendor will change the UpgradeCode. If they do, then Intune will treat the new MSI file as a new/unique application. Depending on the application vendor's code in the new installer file, it may or may not replace the outdated version; it may be installed as a side-by-side application.


  1. Inspect the updated MSI file using an MSI viewer program like Orca.

  2. Ensure that the UpgradeCode is the same as the original MSI.

    1. If it is the same, continue to Step 2.

    2. If it is not the same, continue to Step 2 but know that you may have to create a new app deployment and change the assignment method of the original one to Uninstall.

Step 2: Test the Updated Version



  1. Create a new line of business app listing with the updated MSI installer file.

  2. Set ignore version  to "no."

  3. Assign the deployment to a "test" group that contains the test machines.


Step 3: Deploy the Updated Version

Once you've tested the new version and it passes, then deploy it company-wide.



  1. If the application was originally deployed using Intune, then:

    1. Select the app to edit it.

    2. Select Properties > Edit.

    3. Upload the new MSI file.

    4. Set Ignore Version to No.

    5. Set a reminder to change ignore version to yes after a few weeks; if the app auto-updates itself in the future, we don't want Intune uninstalling it (having ignore version set to yes means that Intune will keep installing the uploaded version).

  2. If the application was not originally deployed using Intune, then:

    1. Create a new app listing and upload the new MSI file.

    2. Set Ignore Version to No.

    3. Assign the app to the appropriate group or to "all devices/users."

    4. Set a reminder to change ignore version to yes after a few weeks; if the app auto-updates itself in the future, we don't want Intune uninstalling it.


Option 2: Use Intune and a PowerShell Script

Alternatively, you can deploy a PowerShell script that uses winget to update the application; you may prefer this option if you did not originally deploy the application using Intune Applications. Remember, winget is a command line tool that Microsoft provides to help install, uninstall, and update applications. To learn more about using winget to update applications; click the link below:



Updating EXE Applications

Option 1: Use Intune and a Win32 App

Remember that you cannot upload EXE applications directly to Intune but rather first convert them to the Intunewin file format. Click the link below to review.




Step 1: Test the Updated Version



  1. Create a new Windows App (Win32) listing with the updated intunewin installer file.

  2. Assign the deployment to a "test" group that contains the test machines.

  3. In the Supersedence section, add the original Win32 application if the old version was deployed using Intune. The installer will most likely update the existing version, but if not, then select yes under Uninstall Previous Version.

Using Supersedence to Uninstall previous versions of an application in Intune.

If the Intune dashboard shows a successful deployment, view the test machines to see if the new version replaced the old one.

  • If not, you'll most likely need to perform the uninstall and install method. This involves two Win32 app deployments: the original one and the one you just created. Ensure that Yes is selected under the Uninstall previous version in the Supersedence section of the new app deployment. You can also use a PowerShell script to uninstall the old version. Click here to learn more.

  • If yes, then continue to step 2.


Step 2: Deploy the Updated Version

If the test is successful and the new version uninstalls/updates the old version, you can change the Assignment method on the new app to the appropriate group or all devices/users.


Option 2: Use Intune and a PowerShell Script

Alternatively, you can deploy a PowerShell script that uses winget to update the application; you may prefer this option if you did not originally deploy the application using Intune Applications. Remember, winget is a command line tool that Microsoft provides to help install, uninstall, and update applications. To learn more about using winget to update applications; click the link below:





Cover picture provided by Freepik.


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