Mergers and acquisitions are often discussed in terms of financial outcomes, market expansion, and organizational restructuring. However, behind the scenes, IT teams face a very different reality. One of the most overlooked but critical areas is application packaging in mergers and acquisitions.
When two companies come together, their application environments rarely align. Each organization brings its own tools, standards, formats, and workflows. What initially looks like a straightforward consolidation quickly turns into a complex process of evaluation, standardization, and migration.
This article explores what actually happens to software packaging during an M&A, why it becomes challenging, and how organizations can approach it strategically.
Why Application Packaging in Mergers and Acquisitions Becomes a Challenge
At its core, application packaging ensures that software can be deployed reliably across an organization’s endpoints. In stable environments, this process is already structured and standardized. In M&A scenarios, that structure breaks down.
The main issue is duplication and inconsistency. Both companies typically have their own packaging formats, such as MSI, MSIX, or IntuneWin, along with different deployment tools like Microsoft Intune or Configuration Manager. These environments are rarely compatible out of the box.
As a result, IT teams must deal with:
- Duplicate applications packaged in different formats
- Conflicting packaging standards and naming conventions
- Separate deployment infrastructures
- Inconsistent documentation and metadata
This fragmentation makes it difficult to determine which packages should be kept, reworked, or retired.
The Hidden Complexity of Overlapping Application Portfolios
One of the first steps in any M&A integration is creating a unified application portfolio. However, this is easier said than done.
Both organizations often use similar tools, but in different versions or configurations. For example, .NET Framework versions may need to run side by side to support different applications, while Microsoft Visual C++ Redistributables are installed in multiple versions to meet specific dependencies. Even widely used tools like Adobe Acrobat Reader or Microsoft Office can differ in release tracks, update channels, or packaging formats, depending on how they were managed in each environment.
This leads to a situation where:
- It becomes unclear which version should be treated as the standard
- Existing packages cannot be reused without validation or rework
- Application behavior may differ across environments after deployment
- Troubleshooting becomes more complex due to inconsistent setups
Without a clear overview, teams risk maintaining redundant packages or, worse, deploying incompatible versions across the environment.
Standardization: The First Major Turning Point
To move forward, organizations must define a single packaging standard. This is one of the most critical decisions in application packaging in mergers and acquisitions.
Standardization typically involves selecting:
- A primary packaging format (e.g., MSI, MSIX, IntuneWin)
- A unified deployment platform (e.g., Intune or SCCM)
- Naming conventions and versioning rules
- Documentation and metadata requirements
This step is not just technical – it is strategic. Choosing the wrong standard can slow down integration and create long-term inefficiencies.
However, standardization also introduces a significant workload. Existing packages from both organizations often need to be repackaged to align with the new standards.
Repackaging at Scale: The Real Bottleneck
Once standards are defined, the next challenge is execution. Repackaging applications takes time, especially when there are hundreds or even thousands of them.
Each package has to go through several steps. It needs to be checked for compatibility, adjusted to fit the new standards, tested in a controlled environment, and properly documented. None of this is optional, and it all adds up quickly.
This is where things start to slow down. Internal IT teams are usually already busy with other parts of the integration, so repackaging becomes a bottleneck. What looks like a simple migration at first can easily turn into months of work.
Deployment Tool Consolidation and Its Impact
Another key aspect of application packaging in mergers and acquisitions is the consolidation of deployment tools.
If one company uses Microsoft Intune and the other relies on Configuration Manager, a decision must be made. Many organizations move toward cloud-based solutions like Intune, but this transition is not immediate.
Packages created for one platform often need to be converted or adjusted for another. For example:
- SCCM packages may need to be converted into IntuneWin format
- Detection rules and installation commands must be redefined
- Deployment logic and targeting strategies change
This adds another layer of complexity to the packaging process and increases the risk of deployment issues.
Documentation Gaps and Knowledge Loss
One of the less visible challenges in application packaging in mergers and acquisitions is the loss of knowledge.
Packaging processes are often undocumented or only partially documented. When teams merge or restructure, key details about how packages were built and maintained can disappear with them.
As a result, existing packages become harder to understand and maintain. Troubleshooting takes longer, onboarding slows down, and changes require additional effort. Over time, this limits standardization and makes the environment more difficult to manage consistently.
The Role of Automation and External Support
Given the scale and complexity of M&A integrations, many organizations turn to automation or external support to keep the process manageable.
Automation helps reduce the amount of manual work involved. It allows teams to standardize packaging workflows, detect new application versions, and handle repetitive tasks more efficiently. Instead of rebuilding every package from scratch, teams can move faster and work with a more consistent process.
At the same time, internal capacity often becomes a constraint. Even with automation, reviewing, rebuilding, and testing large numbers of applications takes time. During an M&A, this effort quickly competes with other priorities, slowing down the entire integration.
This is where external support becomes valuable. Rather than replacing internal teams, it extends their capacity and brings in additional expertise exactly when it is needed. This makes it easier to maintain progress without overloading the team or compromising quality.
In practice, some solutions combine both approaches. For example, Apptimized enables teams to automate packaging workflows while also providing ready-to-deploy, validated packages and support for large-scale transitions, including conversion to formats used in environments like Intune. This allows organizations to handle large volumes of applications more efficiently while keeping packaging standards consistent.
This combination becomes especially valuable when timelines are tight and the number of applications is high, helping teams reduce bottlenecks while staying in control of the process.
Conclusion
Application packaging during mergers is rarely just a technical task. It sits at the center of integration, affecting how quickly systems can be aligned, how reliably applications can be deployed, and how smoothly teams can move forward after the merger.
What makes it challenging is not a single issue, but the combination of overlapping applications, inconsistent standards, and the sheer volume of work required to bring everything together. Without a structured approach, these factors quickly turn packaging into a bottleneck that slows down the entire integration.
The good news is that this process can be managed more effectively with the right balance of standardization, automation, and additional support when needed. Organizations that approach packaging as a strategic part of M&A are better positioned to reduce risks, maintain consistency, and keep timelines under control.
If you’re currently facing similar challenges or planning an upcoming integration, it’s worth taking a closer look at how your packaging process is set up. Book a demo with our specialist to see how you can simplify application packaging and move forward with a more structured, scalable approach.