Intune Application Deployment : 4 different ways to Install Applications on Windows Machines

Introduction

Microsoft Intune is a powerful cloud-based management solution that allows IT administrators to deploy, manage, and monitor applications on Windows devices seamlessly. Deploying applications through Intune ensures that software is installed consistently, updated regularly, and compliant with enterprise policies.

In this guide, we will explore the different methods available to install applications on Windows machines using Intune, including Store apps, Win32 apps, MSI packages, and scripts.

1 – Using Microsoft Store Apps

Microsoft Intune allows administrators to deploy applications directly from the Microsoft Store. This method is ideal for deploying commonly used business applications such as Microsoft 365 Apps, OneDrive, and Edge.

Steps to Deploy Microsoft Store Apps in Intune

Choose Microsoft Store app (new)

Log in to the Intune Admin Center

Navigate to Apps > Windows and click on Add

1. Click Select and search for the desired app (M365 apps for my example)
2. Configure assignment settings (Available, Required, or Uninstall)
3. Click Next

• Install behavior : Select ‘System‘ to install this app for all users if supported. Select ‘User‘ to install this app for the logged-in user on the device.
• Show this as a featured app in the Company Portal : Featured apps are prominently placed in Company Portal so that users can quickly get to them.
• Click Next
• Assign users then create.

Pros and Cons

✅ Easy to deploy and update automatically

✅ No need for complex packaging

❌ Limited to applications available in the Microsoft Store

2 – Deploying MSI and EXE Applications

Intune supports the deployment of .msi and .exe applications, which are commonly used for software installation.

This method is preferred for applications with built-in silent installation support.

Steps to Deploy MSI and EXE Applications in Intune

1. Prepare the MSI package
2. Log in to the Intune Admin Center
3. Navigate to Apps > Windows and click on Add
4. Choose “Line-of-business app”
5. Clic “Select“

• Select you application from your local disk or network mapped drive, then click OK

Pros and Cons

✅ Easier packaging compared to Win32 apps

✅ Native support for enterprise applications

❌ Limited flexibility compared to Win32 app packaging

3 – Deploying Win32 Applications

For more complex applications, Intune supports Win32 apps, allowing administrators to install .exe or .msi applications with custom installation parameters.

This method is preferred for customized applications or for non packaged apps (folder with files)

Steps to Deploy Win32 Applications in Intune

1. Prepare the Application for Deployment

• Convert the installer to .intunewin format using the IntuneWinAppUtil.exe tool (download it from here : Github Link)
• Run the following command :

IntuneWinAppUtil -c <setup_folder> -s <source_setup_file> -o <output_folder> <-q>

Here is full command line parameters :

in this example I will prepare Trend Micro inrunewin file :

After preparing .intunewin file :

1. Log in to the Intune Admin Center
2. Navigate to Apps > Windows and click on Add
3. Select Windows app (Win32) then clic Select

• Select intunewin file the click OK

• Select “Next” , Assign users then create

Pros and Cons

✅ Ideal for complex installations with dependencies

✅ Supports custom scripts and parameters

❌ Requires extra packaging steps

4 – Installing Applications via PowerShell Scripts

For applications that require custom installation logic, PowerShell scripts can be used to deploy software via Intune.

Steps to Deploy Applications Using PowerShell Scripts

A – Prepare the PowerShell Script

Example script for installing an app :

Start-Process -FilePath "C:\Temp\setup.exe" -ArgumentList "/silent" -Wait

B – Upload to Intune

• Log in to the Intune Admin Center
• Navigate to Devices > Scripts and remediations > Plateform scripts > Add
• Select Windows 10 and later

• Upload the .ps1 script

• Assign users and Deploy.

Pros and Cons

✅ Highly flexible

✅ Can be used for configuration as well

❌ Requires scripting expertise

5 – Conclusion

Microsoft Intune provides multiple ways to deploy applications on Windows devices, from simple MSI installations to advanced Win32 packaging and scripting. Choosing the right method depends on the complexity of the application, management requirements, and user needs.

If you are managing a large fleet of devices, leveraging Win32 Apps and Microsoft Store for Business will provide the best balance between automation and flexibility. For simpler deployments, MSI installations and PowerShell scripts offer quick and effective solutions.

By following this guide, you can streamline your Intune app deployment strategy and ensure a seamless experience for your users.

Very important :

• Maximum size limit for a Win32 app package that can be uploaded to Intune is 8 GB
• Never mix Win32 and LOB apps during autopilot enrollement because both of them are using Trusted installer service : Microsoft Link

Thanks