Jhonny Marques
Technical Consultant|Kerv Transform
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Get in touchPublished 30/01/25 under:
Effective application management is a cornerstone of modern IT operations, helping organisations maintain security, improve efficiency, and enhance user experience.
As part of our Mastering Microsoft Intune webinar series, we recently explored the crucial topic of Application Packaging in Microsoft Intune. This session provided an in-depth look at why packaging is necessary, how to execute it, and best practices for deployment. Below, we recap the key takeaways and insights shared during the webinar.
Watch the webinar to see in-depth demos and best practice for application packaging within Microsoft Intune.Ctrl Alt Innovate Webinar: Application Packaging
Why Application Packaging Matters
Many business-critical applications are not available in official app stores, or they rely on older installation methods that do not support automatic updates. This can lead to inefficient deployment, security vulnerabilities, and compliance challenges. By packaging applications for Intune, organisations gain centralised management, enabling IT teams to deploy and update applications across all devices from a single platform. This approach also allows for precise version control, ensuring compliance and compatibility, while automated deployment reduces manual intervention, freeing up IT resources. Furthermore, packaging applications through Intune helps enhance security by enforcing consistent policies and keeping applications updated.
Key benefits of application packaging include:
- Centralised management – Deploy and update applications across all devices efficiently.
- Version control – Maintain compliance and compatibility with controlled updates.
- Automated deployment – Reduce IT workload by streamlining installation processes.
- Enhanced security – Ensure applications remain secure with centralised policies.
Understanding the Application Lifecycle in Intune
Managing applications in Intune follows a structured lifecycle:
- Adding the App – Applications can be sourced from the Microsoft Store, Apple App Store, Google Play Store, or through custom Line-of-Business (LOB) applications such as MSI or EXE installers.
- Configuring the App – Adjusting settings to ensure functionality, security, and compliance within the organisation.
- Protecting the App – Applying security policies such as App Protection Policies and Conditional Access.
- Assigning the App – Deploying applications to users, devices, or specific groups.
- Deploying the App – Rolling out apps automatically or making them available via the Company Portal.
- Monitoring & Managing – Tracking compliance, troubleshooting issues, and managing updates.
- Retiring the App – Removing outdated or unnecessary applications and ensuring no residual corporate data remains.
By following this structured approach, organisations can ensure that applications are efficiently managed from deployment to retirement, minimising security risks and IT overhead.
Packaging Applications for Microsoft Intune
When applications are not available in official app stores, IT admins need to package them into a format that Intune can deploy. This is where the Intune App Preparation Tool becomes essential. This tool allows IT administrators to take installation files such as EXE or MSI and convert them into an .intunewin package.
Steps to Package an Application for Intune:
- Gather Installation Files – Collect the necessary EXE, MSI, or additional dependencies such as DLLs or configuration files.
- Run the Intune App Preparation Tool – This Microsoft-provided tool converts application installers into the .intunewin format, which is compatible with Intune.
- Configure Detection Rules – Set up validation mechanisms to confirm successful installation (e.g., registry entries, file paths, MSI product codes).
- Define Installation & Uninstallation Commands – Ensure that Intune can correctly install and remove the application when needed.
- Upload the Packaged App to Intune – Navigate to Intune Admin Centre and add the newly created .intunewin package.
- Assign and Deploy the Application – Select deployment strategies such as Required Installations or Self-Service via the Company Portal.
Deployment Strategies & Best Practices
Deploying applications effectively requires careful planning and adherence to best practices. One of the key decisions is choosing between:
- Required Installation – Automatically push critical applications to devices without user interaction.
- Available for Users – Allow employees to install applications on-demand through the Company Portal.
Phased Deployment Approach:
- Testing (IT Admins) – Validate silent installs, detection logic, and dependencies.
- Pilot Deployment – Roll out to a small user group to confirm functionality.
- Full Rollout – Expand deployment across departments or the entire organisation.
Maintaining version control is also crucial in application packaging. Each update should be properly documented, and previous versions should be retained for rollback purposes in case issues arise. Proper detection rules should be configured to avoid installation loops or incomplete deployments. In addition, organisations should leverage Intune’s monitoring tools to track deployment status, troubleshoot issues, and ensure compliance.
Common Questions Answered
During the webinar, attendees raised several valuable questions.
Can we include licence files in Intune packages?
Yes! During the packaging process, configuration files, licence keys, and dependencies can be bundled together, ensuring they are deployed together.
How can we ensure apps are updated automatically?
Store apps update automatically, but for packaged applications, version control must be managed manually. However, Intune’s Supersedence feature enables seamless upgrades, allowing new versions to replace older ones automatically.
Watch the webinar to see in-depth demos and best practice for application packaging within Microsoft Intune.Ctrl Alt Innovate Webinar: Application Packaging
Intune Support
Application packaging in Intune is a powerful way to streamline app management, improve security, and reduce IT overhead. By following best practices and leveraging the right tools, organisations can ensure smooth deployment and minimal user disruption.
Have questions or need help optimising your Intune environment? Contact us today!
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