How to Package Applications for Microsoft Intune

Deploying applications through Intune can streamline your IT processes. It allows you to manage and distribute software efficiently. This guide will walk you through packaging an application for Intune deployment.

Introduction

Microsoft Intune has become the preferred endpoint management solution for organisations adopting cloud-first device management. As businesses transition from traditional on-premises management tools such as Microsoft Configuration Manager (SCCM) to Microsoft Intune, application packaging plays a critical role in ensuring software is deployed consistently, securely, and with minimal disruption to users.

Whether you're deploying Microsoft 365 Apps, a line-of-business application, or a third-party installer, proper packaging ensures applications install reliably, update correctly, and can be removed cleanly when no longer required.

This guide explains the complete process of preparing, packaging, deploying, and maintaining applications in Microsoft Intune using industry best practices.

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What Is Application Packaging?

Application packaging is the process of preparing software for automated deployment across managed devices.

Rather than manually installing applications on each computer, packaging allows administrators to create standardised installation packages that can be deployed remotely using Microsoft Intune.

A well-packaged application should:

Install silently without user interaction
Support automated deployment
Detect whether the application is already installed
Uninstall cleanly
Support version control and updates
Minimise user disruption
For enterprise environments, packaging also ensures consistency across thousands of devices while reducing the risk of installation errors.

Supported Application Types in Microsoft Intune
Microsoft Intune supports several application formats, each suited to different deployment scenarios.

Win32 Applications (.intunewin)
The Win32 application format is the most commonly used for enterprise deployments. It supports traditional desktop applications packaged as MSI or EXE installers and provides advanced deployment features such as dependencies, supersedence, requirement rules, and custom detection methods.

Win32 apps are ideal for:

Legacy desktop applications
Third-party software
Custom business applications
Software requiring installation scripts
Applications with prerequisites
 
MSI Applications
MSI packages are Windows Installer files that include built-in installation logic, repair functionality, and uninstall support. They are widely used for enterprise software because they support silent installation and integrate well with management tools.

Common characteristics include:

Product Codes and Upgrade Codes
Silent installation using standard switches
Automatic repair capabilities
Consistent uninstall behaviour
 
MSIX Applications
MSIX is Microsoft's modern application packaging format designed for improved security, reliability, and application lifecycle management.

Key advantages include:

Containerised installations
Clean uninstalls
Digital signing
Reduced system changes
Better compatibility with Azure Virtual Desktop

MSIX is particularly well suited to modern Windows 11 deployments and cloud-managed environments.

 
Microsoft Store Applications
Microsoft Intune can also deploy applications directly from the Microsoft Store, making it easier to manage commonly used software without maintaining installation files.

Examples include:

Company Portal
Microsoft Whiteboard
Power BI
Microsoft To Do
 
Step 1: Assess the Application
Before packaging any application, perform a technical assessment to understand its deployment requirements.

Questions to ask include:

What installer format is provided?
MSI
EXE
MSIX
Setup.exe
ZIP archive
Does the installer support silent installation?

Examples:

 setup.exe /silent
setup.exe /S
msiexec /i app.msi /qn
 
Are administrator privileges required?
Determine whether the application installs per-user or per-machine.

Are there any prerequisites?

Examples include:

.NET Framework
Visual C++ Redistributables
Java Runtime
SQL Native Client
Microsoft Edge WebView2 Runtime
Installing prerequisites before the main application helps avoid deployment failures.

 
Step 2: Understand Application Dependencies
Many enterprise applications rely on external components.

These may include:

SQL Server databases
Oracle databases
File shares
Licence servers
LDAP or LDAPS
Active Directory
Entra ID authentication
Web services
APIs

Documenting these dependencies early prevents issues during deployment and testing.

 Step 3: Test the Installer Manually
Before creating an Intune package, install the application manually on a clean test device.

During testing, confirm:

Installation completes successfully
No unexpected prompts appear
Required services are created
Registry entries are added
Files install to expected locations
Application launches correctly
Licensing works
Printing functions correctly (if applicable)
This baseline testing makes it easier to troubleshoot deployment issues later.

 
Step 4: Prepare the Source Files
Create a structured source folder containing only the files required for deployment.

A typical structure might look like:

 
ApplicationName\
├── Source
│   ├── setup.exe
│   ├── config.xml
│   ├── licence.dat
│   └── install.cmd
├── Detection
└── Documentation
 
Keep installation scripts, documentation, and source files organised to simplify future updates and version management.

 
Step 5: Create the Win32 Package
Use the Microsoft Win32 Content Prep Tool to convert the application into an .intunewin package.

This tool compresses and encrypts the installation files into a format that Microsoft Intune can distribute securely.

When creating the package:

Select the correct source folder.
Specify the installer file.
Verify the output location.
Record the package version for documentation.
 
Step 6: Upload the Package to Microsoft Intune
In the Microsoft Intune admin centre:

1. Navigate to Apps > Windows > Add.
2. Choose Windows app (Win32).
3. Upload the .intunewin file.
4. Enter application details such as:

Name
Description
Publisher
Category
Logo (optional)

Clear and consistent naming conventions make applications easier to manage and identify.

Step 7: Configure Installation Commands
Specify the silent install and uninstall commands.

For an MSI:

 
Install:
msiexec /i Application.msi /qn /norestart

Uninstall:
msiexec /x {ProductCode} /qn
 
For an EXE, use the vendor's documented silent switches.

Always test these commands locally before using them in Intune.

Step 8: Configure Detection Rules
Detection rules allow Intune to determine whether an application is already installed.

Common methods include:

MSI product code
File existence
Registry key
Custom PowerShell script
Accurate detection rules prevent unnecessary reinstalls and ensure compliance reporting is reliable.

 
Step 9: Configure Requirement Rules
Requirement rules define which devices are eligible to receive the application.

Typical criteria include:

Windows 10 or Windows 11
64-bit architecture
Minimum free disk space
Minimum RAM
Operating system edition

This helps avoid deploying incompatible applications to unsupported devices.

Step 10: Configure Dependencies and Supersedence
If an application requires another application to be installed first, configure it as a dependency.

Examples:

Visual C++ Redistributable
Microsoft Edge WebView2 Runtime
SQL Server Native Client
Supersedence allows a newer version of an application to replace an older version automatically, simplifying application lifecycle management.

 
Step 11: Assign the Application
Deploy applications to Microsoft Entra ID groups based on business requirements.

Common assignment types include:

Required: Automatically installs on targeted devices or users.
Available: Users can install the application from the Company Portal.
Uninstall: Removes the application from targeted devices.
Using dynamic groups can help automate application assignments based on device attributes or user roles.

 
Step 12: Test the Deployment
Before rolling out to the entire organisation, validate the package with a pilot group.

Verify:

Installation completes successfully.
The application launches correctly.
User settings are retained after restart.
Updates function as expected.
Uninstallation is successful.
Intune reports the installation status accurately.
Testing across different hardware models and network conditions helps identify issues before a wider deployment.

 
Common Packaging Challenges
Enterprise application packaging often involves challenges such as:

Missing silent install switches.
Incorrect detection rules.
Applications requiring user interaction.
Hard-coded installation paths.
Per-user installers.
Reboot requirements.
Legacy applications that are not cloud-ready.
Documenting known issues and workarounds is essential for long-term support.

 
Best Practices
To achieve consistent and reliable deployments:

Standardise packaging processes.
Maintain version-controlled documentation.
Test every package in a clean environment.
Use meaningful naming conventions.
Keep detection rules simple and reliable.
Validate rollback procedures.
Monitor deployment success rates in Intune.
Review packages regularly to remove obsolete applications.
A structured packaging process reduces deployment failures and improves the end-user experience.

 
Conclusion
Application packaging is a foundational component of successful Microsoft Intune deployments. By following a structured process that includes assessment, dependency analysis, packaging, testing, and controlled deployment, organisations can deliver applications consistently while reducing support overhead.

As organisations continue to modernise endpoint management and adopt Windows 11 and cloud-native management, investing in robust application packaging practices ensures software remains secure, maintainable, and ready for future change.

 
Frequently Asked Questions
What is the difference between an MSI and a Win32 app in Intune?
An MSI is an installer format, while a Win32 app in Intune is a packaged deployment format (.intunewin) that can contain MSI, EXE, scripts, and supporting files.

Can Intune deploy EXE applications?
Yes. EXE installers can be packaged as Win32 apps, provided they support unattended installation.

Should I use MSIX instead of MSI?
MSIX is Microsoft's preferred modern packaging format where supported, but many enterprise applications are still distributed as MSI or EXE. The appropriate choice depends on the application's compatibility and vendor support.

Do I need Microsoft Intune to deploy Win32 applications?
Yes. Win32 app deployment is a feature of Microsoft Intune and requires managed Windows devices enrolled in Intune.

 
Need Help with Microsoft Intune Application Packaging?
Cloud Breeze helps organisations package, test, and deploy Windows applications using Microsoft Intune, MSIX, MSI, and Win32 technologies. Whether you're modernising endpoint management, migrating from SCCM, or preparing applications for Azure Virtual Desktop, our consultants can help you deliver secure and reliable application deployments at scale.

Contact Cloud Breeze to discuss your application packaging and endpoint management requirements.