Managing a large estate of Windows applications in an enterprise environment is a complex task. Traditional software deployments often involve a mix of installers (EXE, MSI, scripts) that can lead to inconsistent environments, security risks, and high support overhead. To address these challenges, many organizations are moving to modern application packaging formats – specifically MSIX and Microsoft Intune Win32 packages – and adopting a centralized, Business-as-Usual (BAU) methodology for Windows application management.
This approach means every Windows application is packaged in a standard format and maintained in a continuous fashion rather than through sporadic, ad-hoc, massive projects. The result is a more secure, manageable, and cost-effective application environment. Below, we explore the advantages of packaging all Windows applications with MSIX or Intune Win32, and how a centralized BAU application management strategy benefits both the business and end users.
Primary benefits of packaging all apps to the business overall:
Secondary benefits of packaging all apps for end users:
Adopting modern Windows application packaging and centralized management delivers numerous tangible benefits to the business:
Modern packages dramatically improve enterprise security. MSIX packages are tamper-proof – they must be digitally signed and are validated before installation, greatly reducing the risk of malware or unauthorized code execution. The containerization in MSIX means apps run isolated, preventing them from modifying the OS or other applications, which protects system integrity and data.
Intune’s centralized control further ensures that users cannot install unapproved software or outdated versions; all software is deployed through IT-managed channels. By restricting admin privileges and funneling Windows apps through a controlled pipeline, the organization closes the door to shadow IT and malicious installs.
Security patches and updates are also rolled out uniformly to all devices via the central system, ensuring no device is left unpatched, a critical factor in preventing breaches. In summary, packaging every app through MSIX/Intune yields a safer IT environment with far fewer avenues for security compromise.
Standardizing on MSIX and Intune Win32 streamlines the entire application lifecycle. IT administrators package a Windows app once and can then deploy or update it everywhere with a few clicks, instead of touching each machine or dealing with manual installs.
Modern management tools provide automation for tasks like installing updates or uninstalling old versions across the fleet. This centralized deployment is far more efficient, saving significant time and IT effort. It also reduces human error – automated, silent installs via Intune or Configuration Manager ensure consistency, whereas manual installations might be prone to mistakes or omissions.
Additionally, packaging processes typically include rigorous testing (in dev/UAT stages) before rollout, which means by the time the software reaches production, most issues have been ironed out. As a result, day-to-day continuous application management becomes a predictable, well-oiled operation instead of a reactive fire-fighting exercise.
A centralized packaging approach gives IT strong control over company software assets. The IT team can enforce standard configurations and versions for all users, adhering to internal standards and industry regulations. By controlling exactly which applications and versions are installed on endpoints, organizations ensure license compliance and reduce unauthorized software usage.
This level of control is often necessary for regulatory compliance, auditing, and reporting. For example:
Enterprise IT teams have to support a constantly growing and changing user base, remote, hybrid, office workers, and multiple device types – a task that manual software management cannot easily scale to. Packaging Windows applications in MSIX/Intune Win32 and using centralized distribution allows virtually unlimited scaling. Whether deploying an app to 100 machines or 10,000, the effort is almost the same: the package is uploaded once and pushed through Intune or another management tool.
Cloud-based content distribution (in Intune or via content delivery networks) means even geographically dispersed endpoints get the software without a hitch. This “package once, deploy everywhere” approach is inherently scalable. Automated deployment pipelines can handle large numbers of devices with ease, which is crucial for growing organizations or those with widely distributed workforces.
Moreover, modern formats like MSIX optimize distribution by downloading only incremental changes, conserving bandwidth and speeding up rollouts for large deployments. The net effect is that the business can efficiently roll out new apps or updates enterprise-wide in a controlled timeframe, supporting growth and change without needing a proportional increase in IT headcount.
Although establishing an application packaging practice has upfront costs, it yields significant ROI in cost savings over time. First, it reduces manual work like installations and troubleshooting, which directly cuts labor costs. With standardized packages, helpdesk calls and tickets significantly drop, saving time and resources.
Second, by preventing security incidents and ensuring patches are applied, companies avoid the potentially enormous costs associated with breaches or downtime from malware – a preventative savings that is hard to overstate.
Third, the improved efficiency and scalability translate to productivity gains for IT staff, who can manage more with less effort. They can focus on higher-value projects rather than fighting fires, which is an opportunity cost saving.
Finally, using modern cloud-based management like Intune can reduce infrastructure costs: there is less need for on-premises servers or site visits to deploy software, which lowers operating expenses.
In short, a well-implemented packaging strategy reduces ongoing administration and support costs while minimizing expensive disruptions.
While the business case is compelling on its own, it’s also important to note how end users benefit from enterprise-wide application packaging.
Users experience more reliable Windows applications with fewer errors. Packaged apps undergo thorough testing and are delivered in a controlled manner, so it’s rare for users to encounter missing dependencies or misconfigurations that would cause crashes.
MSIX’s containerization further prevents apps from interfering with each other or the OS, which means less instability over time (no more “DLL hell” or broken apps after installing another program). In fact, MSIX boasts a 99.96% successful installation rate across millions of installs, with a guaranteed clean uninstall that leaves no stray files or registry entries. This level of reliability directly translates to less downtime or frustration for employees trying to get their work done.
Packaging every Windows app ensures that all users have the same version and configuration of software, which creates a consistent experience across the organization. When an employee logs into a new device or remote location, the required applications can be auto-installed via Intune with standardized settings, so they can start work quickly with a familiar setup.
This consistency reduces compatibility issues when sharing files or collaborating – everyone is on the same edition of Office, design software, etc. It also means training and documentation can be unified and only updated when needed. From the user’s perspective, things “just work” because IT has eliminated the randomness of manual installs or outdated software.
With centralized packaging, software installations and updates are often executed silently in the background, without needing user intervention or causing work stoppage. End users no longer have to perform installs themselves or deal with confusing prompts – applications deploy or update automatically via the management tool.
Updates that fix bugs or add features reach users faster, because IT can push them as soon as they’re available and have been tested, without needing to wait for each user to update. In cases where a critical patch is needed, Intune Win32 deployment can even force-install an update to all devices quickly, which ultimately keeps users safer and productive with up-to-date tools. This leads to a smooth employee experience where they encounter fewer interruptions and can trust that they always have the latest, most secure version of the software they need.
Overall, by improving reliability and consistency, the modern packaging approach enhances employee productivity and satisfaction. Users spend less time calling the helpdesk or troubleshooting software glitches, and more time doing their jobs with stable tools – a quiet but significant boost to morale and efficiency.
Many enterprises have embraced these modern packaging practices. For instance, large IT organizations often manage thousands of applications and have made packaging a standard practice to handle this scale. In one case, a large financial institution has over 2,000 Windows applications, each requiring frequent updates. They realized that to keep pace with the Windows-as-a-Service model, they would need a centralized, continuous application management process. By investing in proper tooling, they were able to save thousands of manual labor hours and continuously roll out updates without disrupting users or business operations.
Software vendors are also providing applications in enterprise-friendly packaged formats. A prominent example is Microsoft offering the Office 365 Apps suite and Microsoft Teams in MSIX format for enterprise deployment. This allows organizations to easily distribute these critical productivity tools via Intune or Configuration Manager with all the benefits of MSIX, such as isolation and differential updates.
Likewise, many third-party software providers and internal development teams are converting installers to MSIX to take advantage of its security and ease of management. Where MSIX isn’t available, IT teams use the Intune Win32 wrapping tool to package traditional installers, for applications like Adobe Acrobat, Zoom, or custom in-house apps, into a format ready for Intune deployment.
Real-world use cases underscore key benefits. For example, after adopting Intune Win32 for application deployment, some organizations report dramatically reduced support tickets related to software installation, as noted above.
In the case of security, organizations in regulated industries like healthcare and government have used MSIX packaging to enforce digital signing and isolation of legacy apps that were previously hard to control. This helped them meet compliance mandates such as ensuring no unauthorized software runs on endpoints and that all apps are up-to-date with security patches, in a streamlined way.
Even in virtual desktop environments, technologies like MSIX App Attach (in Azure Virtual Desktop) allow packaged apps to be dynamically attached to user sessions. This means a smaller base image and the ability to rapidly provision or update apps for thousands of virtual users without re-imaging – a clear scalability win.
These examples illustrate that whether it’s a cloud-first modern desktop environment using Intune or a large on-premises setup using Configuration Manager, packaging every application yields real operational improvements. Organizations achieve a more controlled, secure, and efficient software delivery process, which in turn supports business agility. As best practices from Microsoft and industry experts show, the path forward for enterprise IT is to treat application management not as a tedious overhead, but as a strategic asset – one that modern packaging formats and centralized, BAU processes make possible.
Packaging all Windows applications in modern formats like MSIX and Intune Win32, and managing them through a centralized BAU methodology, is becoming the gold standard for enterprise IT. This approach transforms application management from a source of headaches into a streamlined operation that delivers security, compliance, and cost-efficiency for the business, as well as reliability and consistency for end users.
By investing in modern packaging, enterprises can reduce risk and complexity today while setting the stage for easier scalability and innovation tomorrow. In an era where both cyber threats and the pace of software updates are accelerating, having a robust application packaging and deployment strategy is not just an IT concern but a business imperative. The evidence from industry practices and Microsoft’s own tools and guidance is clear – a centralized, packaged-by-default application estate is key to a secure, agile, and cost-effective enterprise IT environment.
All told, modern application packaging provides a win-win: IT departments gain control and efficiency, and users get a safer, more seamless computing experience that lets them focus on their work rather than their software.