How to deploy .exe applications using Intune

When you download an application from software vendor’s website. The application installer can be in the form of .msi file or .exe file. Intune provides different ways in which you can deploy the applications on end user devices.

Deployment is MSI files using Intune can also be done in two ways. You can use Line-of-business app method for deploying a simple MSI application on windows devices.

However, if your MSI app installation process is more complex for example: you need to deploy multiple MSI files with additional configuration using pre or post scripts or if you have an MSI + MST files. you can also use Windows app (Win32) app deployment method to deploy an MSI files.

It not that Win32 app deployment for a simple MSI file would not work, but if there is a simpler approach and method provided then its best to use that one.

But In this blog post, we will see how you can deploy an .exe application using Intune. For deploying an .exe app, you need to use Windows app (Win32) app deployment method which requires .exe file to be wrapped in .INTUNEWIN file first and then upload it to Microsoft endpoint manager admin center to deploy.

There are few Prerequisites we need to know before proceeding with Windows app (Win32) app deployment. Let’s check:

  • Windows 10 version 1607 or later.
  • Devices must be enrolled in Intune and either:
    • Azure AD registered
    • Azure AD joined
    • Hybrid Azure AD joined
  • Application size must not be greater than 8 GB.

Download the app from software vendor’s website

First step is to download latest version or the of the application or the version of the application you want to deploy from vendor’s website. If you have already downloaded the app then you can proceed to the next step.

For showing you the deployment of .exe files using Intune, I will be using Notepad++ application as an example app. However, you can use the steps given in this blog post to deploy any .exe file.

Finding Silent Command line Install / Uninstall switches for an app

Most of the applications can be managed using command line. Therefore, we need to check application documentation to find Install and Uninstall switches. Depending upon each vendor, this information may be given in Installation Manual or User Manual.

For Notepad ++ app, I was able to find this information from Notepad ++ Online User Manual. Scroll down on this link and find Installer Options where it provides /S switch to install the application silently. Please make sure its uppercase S not lowercase.

For Uninstallation, you just need to use Uninstall.exe file copied in the installation folder with /S switch for Silent Uninstall.

Notepad ++ Silent Install command

npp.8.4.9.Installer.x64.exe /S

Notepad ++ Silent Uninstall command

C:\Program Files\Notepad++\uninstall.exe” /S

Test Silent Install / Uninstall switches manually on one device

Its always a best practice to test the application locally first on one or two devices manually to see if the installation and Uninstall command line switches are working fine.

Testing Silent Install of Notepad ++ manually on one device

  • Launch Command prompt as administrator on a windows device
  • Change the command prompt location to the folder where notepad ++ exe installer file e.g. npp.8.4.9.Installer.x64.exe is downloaded / copied.
  • Run the .exe file with /S switch to test the installation [Make sure to use UpperCase S].
  • Installation will complete silently without any prompts.
  • Verify if the application has been installed by Going to Start > Run > type appwiz.cpl and press Enter > Check and confirm if the application has been installed successfully.
Notepad ++ application silent Install switch

Testing Silent Uninstall of Notepad ++ manually on one device

Test if the application is getting uninstalled silently using C:\Program Files\Notepad++\uninstall.exe” /S command. Run the command from an elevated command prompt and check if the application is getting uninstalled succesfully. There should not be any User interactive prompts, it should uninstall silently.

If both Installation and Uninstallation switches are working correctly. We can proceed to create a deployment of the .exe file / app from Microsoft endpoint manager admin center / Intune.

Silent Uninstall of Notepad ++ Switch

Create IntuneWin file

As we can deploy an MSI file directly using Intune, there is no way to deploy an .exe file directly, we will have to wrap the .exe file (npp.8.4.9.Installer.x64.exe) into .IntuneWin file format using Microsoft Win32 Content Prep Tool. Here are the steps to create .Intunewin file:

  1. Create a empty folder anywhere in C:\ or D:\ drive and Copy all setup files in that folder. We have created a folder called NotepadPlusSetup, you can name the folder as you like. As we just have one .exe file which installs notepad++ application. We will copy the .exe file in NotepadPlusSetup folder.
Notepad ++ Installer
  1. Download Microsoft Win32 Content Prep Tool. Its a zip file therefore extract its contents into a folder.
  1. Create an empty folder for example C:\output or anywhere you like.
  1. Repackage NotepadPlusSetup folder to .intunewin file using IntuneWinAppUtil.exe which can be located in Microsoft Win32 Content Prep Tool.

You can run one liner command with all the switches specified or you can also run .\IntuneWinApputil.exe to provide you with prompts to specify source folder, setup file and output folder.

.\IntuneWinAppUtil.exe -c "C:\NotepadPlusSetup\" -s npp.8.4.9.Installer.x64.exe -o C:\output
Create IntuneWin file for Win32 app deployment Intune
  1. Now, check C:\output folder to confirm if .Intunewin file has been created successfully.
How to create IntuneWin file

Create Windows app (Win32) package on Intune

Once we have .Intunewin file created successfully. We can use it to create Win32 app deployment which requires .Intunewin file. Let’s check the steps:

Please follow below steps to create Intune Windows app (Win32) app using .IntuneWin file.

  1. Login on Microsoft Intune Admin Center
  2. Click on Apps and then click on All Apps
  3. Click on + Add and Select Windows app (Win32) from the app type

App Information

Click on Select app package file to browse and select npp.8.4.9.Installer.x64.intunewin file and click on OK. On App information tab, provide Information about the Application. Update the NameDescription and Enter the name of the publisher. Click on Next to proceed.

  • Name: Notepad ++ 8.4.9
  • Description: Keep Default or to change click Edit Description
  • Publisher: Notepad++
  • App Version: 8.4.9
Deployment of Notepad++ using Intune Assignments Tab


Provide the Install command, uninstall commandInstall behavior, Device restart behavior. Click on Next to proceed.

  • Install command:  npp.8.4.9.Installer.x64.exe /S
  • Uninstall command: C:\Program Files\Notepad++\uninstall.exe” /S
  • Install behavior: System
  • Device restart behavior: No specific Action
Deployment of Notepad++ using Intune Program Tab


Provide Operating System Architecture and Minimum operating system information. Click on Next to proceed.

  • Operating System Architecture: 64-bit
  • Minimum operating system: Select according to the operating system version being used in your enviornment. For Example: Windows 10 1607.

Detection Rules

Select Manually configure detection rules and click on +Add to add a detection rule.

  • Rules Format: Select Manually configure detection rules
  • Rule Type: File
  • Path: C:\Program Files\Notepad++
  • File or folder: Notepad++.exe
  • Detection method: File or folder exists.
  • Associated with 32-bit app on 64-bit clients: No
Deployment of Notepad++ using Intune Detection Rule


Create an Azure AD Security group which contains users or devices where this application package needs to be deployed. Please note that if you add users into the list, it will deploy this application on all of the users devices joined to Azure and Enrolled into Intune. If you want to deploy the app to specific devices then you should add devices in the Azure AD security group not users.

Make sure to add it to the Required section which will install the application on users system as soon as possible.

Required: Select the groups for which you want to make this app required. Required apps are installed automatically on enrolled devices. Some platforms may have additional prompts for the end user to acknowledge before app installation begins.

To deploy it on all end user devices, You can also click on + Add all devices to target all devices which are enrolled into Intune.

Deployment of Notepad++ using Intune Assignments Tab

Review + Create

Next tab is for Review + Create. Save the application which will start the process of your uploading .intunewin file and also will start the deployment process.

Monitoring the Installation Progress

To check the Installation status of the app, You can follow below steps:

  • From Microsoft Intune admin center, Click on Apps on the left hand side.
  • Click on All apps.
  • Search for the app Notepad ++ 8.4.9 and click on it.

From the Overview page of the application, you can check the status of Installation and Failures. To find more details on which devices the app is pushed successfully, you can also click on Device Install status or User Install status.

Intune Policy Refresh Cycle

The Device will Sync / Check in and download / intstall the application on target device. It may take some time for the process to start. Therefore, if you are testing it on a test device, you can force initiate Intune refresh cycle on the device which will speed up the download and installation process.

Also, you can restart the device first before force initiating the sync. Manual sync is not mandatory on user’s devices as the device check-in process happens automatically. But if you are testing the application on a test device then this can speed up your testing and can save some time.

End User Experience

On the target devices, there is no user interaction with this package. Notepad ++ will be installed on users devices silently.

However, there will be a pop-up notification related to this application if you have “Show all toast notification” setting configured at the time of Intune app assignment. You can disable all toast notifications from Assignments tab under End user notifications setting if you want no notifications or pop-ups related to this deployment.

Verify App Installation using appwiz.cpl

After the application has been installed successfully on the target devices. You can login on one of the user device and use below steps to confirm the application is installed.

  • Go to Start > type Run to search and click on Run [Alternatively press Windows key + R to open run box]
  • Type appwiz.cpl to open Programs and Features.
  • Find the app Notepad ++ or the app you deployed using Intune to confirm if its installed successfully.
  • You can also go to Start and search for the app and launch it as well to test if its working fine.
Verify App Installation using appwiz.cpl

How to uninstall .exe applications using Intune

As we now know the process of deloying exe applications using Intune. What if you want to uninstall this application now using Intune. We had deployed Notepad ++ app by creating a Windows app (Win32) package from Microsoft endpoint manager admin center.

To Uninstall this app, we will use the same Win32 app created for deployment to Uninstall it. Here are the steps for the same:

  • From Microsoft Intune admin center, Click on Apps on the left hand side
  • Click on All apps
  • Search for the app Notepad ++ 8.4.9 and click on it
  • Go to Properties under Manage
  • Click on Edit next to Assignments
  • Remove the devices from Required section and Add it to Uninstall section to Uninstall Notepad ++ 8.4.9

When you add any devices in the Uninstall section of the Assignments tab. Uninstall command provided in the Program tab of the application will be executed on the target devices.

How to uninstall .exe applications using Intune

Frequently Asked Questions (FAQs)

How do I find Silent Install or Uninstall switches for any .exe ?

You can find Silent Install and Uninstall switches of any executable file by checking application Installation manual or User Manual. Try to search for it on the application vendors website to find this information. If you are unable to find this info, you can then contact the vendor or third party from where you purchased the app to provide this information to you.

Some application vendor include Installation manual or Instructions along with the Setup files. Try searching the Installation manual in the Setup files folder as well.

There are some .exe files which can provide the help directly from command prompt. Try typing <appsetupfile>.exe /? or /h or /help. For example FoxitPDFReader121_enu_Setup_Prom.exe /help which provided a popup box with information about all the switches which you can use with this command.

How do I find Silent Install or Uninstall switches for any .exe ?

Can I package a .MSI file using same way as I did for .exe file

Yes, you can package MSI file using Windows app (Win32) method as well like we did for .exe deployment. However this would be a bit complex for a simple MSI app deployment. If you have only one MSI to deploy without any additional scripts to customize the deployment. I would suggest to go for Line-of-business app deployment method for MSI files.

I deployed Win32 app to the device using Intune, but its not Installed

If you have created Windows app (Win32) deployment successfully using the steps given in the blog post and still you are not able to see the app installed on end user devices. There are couple of troubleshooting steps you can perform:

  • If you have just created the deployment and assigned this app to the target device then please wait for couple of hours as it may some time to download and Install the application on target device. Please refer to this blog post for more information.
  • Check the logs from one of the target device to find more information about this deployment. The Intune Management Extension logs are stored at C:\ProgramData\Microsoft\IntuneManagementExtension\Logs location, Log file name is: IntuneManagementExtension.log.  To get the best readability of the log file. Download CMTrace tool and use it to view this log file.
I deployed Win32 app to the device using Intune, but its not Installed


As we have seen how you can deploy an .exe file with Intune using Windows app (Win32) deployment method. You first have to wrap .exe file or setup files into .intunewin file package and then deploy the file using Intune.

Test Silent Install and Uninstall commands of the app to make sure application installation / Uninstallation is working manually from command line. If you are having issues to install the application manually then you will find the same issues when you deploy the app using Intune.