Preparing your Tenant for Pckgr
Best practice tips for a smooth integration
Prepare Your Environment for Pckgr
Before deploying or managing applications with Pckgr, it’s important to ensure your environment is clean, consistent, and aligned with how Pckgr expects to detect and manage applications.
Many environments contain a mix of installer types, architectures, and install contexts; all of which can interfere with reliable detection, updating, or uninstallation.
This guide helps you understand how Pckgr detects apps, why consistency matters, and how to prepare your environment to ensure successful automation.
Why This Matters
When apps are installed inconsistently across devices, for example, using a mix of EXE and MSI installers, or x86 and x64 versions, it creates problems like:
Pckgr not detecting apps properly
Uninstall packages failing silently
Devices reporting incorrect install status
Multiple versions of the same app installed on different machines
Cleaning up your environment before onboarding with Pckgr not only ensures that the updating workflows behave as expected, it is also best practice to have a standardised approach to application management for device continuity.
How Pckgr Detects Applications
Every app in the Pckgr library includes a detection script. This script is uploaded to Intune along with the app package and is used to determine if the app is already present on a device.
Pckgr’s detection scripts differ depending on how the app was originally installed. If the detection script doesn’t find the app at the expected location, Intune will assume the app is not installed, and will perform the update, uninstallation or installation according to that state, which is incorrect. This will cause undesired outcomes on the devices, such as multiple installations of applications in various formats, failed uninstalls or skipped updates.
Common Problems in Real Environments
Here are examples of how inconsistent application installs can create problems:
The same app is installed both per-user and system-wide across different machines
Some devices have the app installed via MSI, others via EXE
Mixture of x64 and x86 versions of the same app across devices
App is manually installed from the vendor site on some machines and deployed through Intune on others
These inconsistencies make it difficult to enforce updates, remove legacy versions, or take over management using Pckgr.
How to Audit Your Environment
To prepare your environment, start by identifying how apps are currently installed across your devices.
Step 1: Export the Installed Applications List
Access Intune’s Discovered Apps list to get a high-level view of all applications installed on all devices that are regiestered to your tenant. This includes all applications, regardless of if they are being managed by Intune or not, providing insight into the installed applications status of the devices.
Admin Centre>Devices>Monitor>Discovered Apps
Step 2: Identify Conflicts
Look for:
The same application listed in different formats (e.g., x64 vs x86, MSI vs EXE)
Per-user installs in
AppData\Local\ProgramsSystem installs in
C:\Program FilesorC:\Program Files (x86)
How to Clean Up the Environment
Once you’ve identified which versions of each app exist, choose the version you want to standardise on.
Step 1: Decide on a Standard Version
For each app, choose:
Installer type (prefer MSI over EXE where possible)
Architecture (prefer x64 unless otherwise needed)
Install context (prefer System Install for manageability, where applicable)
Step 2: Remove the Unwanted Versions
Use Pckgr to deploy uninstall packages. You’ll need to:
Add the correct format of the app to your Pckgr library (Read the Application Library page for an introduction to adding applications).
Applications are split into EXE or MSI formats in the library where applicable. Apps with (User) in the title are User context, those with just their app names are System Context.
Deploy it to Intune with the DIsplay name as 'Removal - App Name'. (Further introduction to deployment available on the Deployment Settings page).
Once the Status of this application says 'Success', click the three-dot menu and select 'View in Intune'.
Assign the app to your target group(s) with the intent set to Uninstall.
For more detail, see: Uninstalling Applications, or alternatively read our Blog Post on the topic.
Step 3: Deploy the Clean Version
Once the old or misaligned versions have been removed, deploy the standard version of the app through Pckgr. This version will now be detectable and manageable across all devices using consistent detection and update logic.
Summary
Cleaning up your environment before deploying with Pckgr ensures that:
Detection scripts work as expected
Uninstall and update actions are successful
All devices remain consistent and easy to manage
By removing inconsistencies in install type, architecture, and context, you enable Pckgr to fully take over lifecycle management of your applications.
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