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Package an .exe for silent deployment: build an .intunewin for Intune

What you are building

Intune deploys Win32 apps from a packaged file named .intunewin. That file is not your .exe renamed—it is output from Microsoft Win32 Content Prep Tool (often called IntuneWinAppUtil), which zips your source folder and encrypts it for upload to Intune.

Before you start

  • Confirm silent switches for your installer (vendor docs, /S, /quiet, /qn, etc.). Intune needs a command that returns quickly and does not prompt the user.
  • Put everything the setup needs in one folder: the .exe (or setup.exe), transforms, config files, or extra MSIs if the vendor requires them side-by-side.

Folder layout

Example:

C:\Packages\MyApp\
  setup.exe
  (optional extra files the vendor requires)

The prep tool will ask for this folder as the source path.

Build the .intunewin

  1. Download Win32 Content Prep Tool from Microsoft (search for “Win32 app packaging tool” / IntuneWinAppUtil).
  2. Run IntuneWinAppUtil.exe (GUI or command line).
  3. Provide:
    • Source folder: C:\Packages\MyApp (folder containing setup.exe).
    • Setup file: the main installer name, e.g. setup.exe.
    • Output folder: where to write the finished package (e.g. C:\Packages\output).
  4. When it finishes, you get MyApp.intunewin (name follows your setup file / folder naming).

Command-line example (same idea; paths may vary):

IntuneWinAppUtil.exe -c C:\Packages\MyApp -s setup.exe -o C:\Packages\output

Upload to Intune

  1. Microsoft Intune admin center → Apps → All apps → Add → Windows app (Win32).
  2. Select your .intunewin file and complete app information.
  3. Install command: full silent command, e.g. setup.exe /S or whatever the vendor documents (test on a VM first).
  4. Uninstall command: use the vendor’s documented uninstall, or MSI product code if the app is an MSI under the hood.
  5. Requirements: OS architecture, minimum Windows version, disk space if needed.
  6. Detection rules: Prefer MSI product code/version if the installer is MSI-based; otherwise file or registry key that proves the app version you deployed. A bad detection rule is the most common reason installs “succeed” but show as failed in Intune.

Assign and test

Assign to a small pilot group first. On a test device, confirm Company Portal or policy triggers install, no UI prompts, and detection shows Installed.

Practical tips

  • Re-run the prep tool whenever you change the installer bits or folder contents; the .intunewin is tied to that snapshot.
  • Keep a short README in your package repo with the exact install, uninstall, and detection values you used—future you will thank you.
  • If the install only works when run from a specific working directory, bake that into a small wrapper script and package the script plus binaries, or use cmd /c / PowerShell with explicit paths in the Intune install command.