Microsoft Intune vs. Configuration Manager for Third-Party Application Patching 

Effective patch management is critical to keep your IT environment secure and running smoothly. Microsoft offers two leading platforms for endpoint management—Intune and Microsoft Configuration Manager (ConfigMgr). In this post, we compare these tools, focusing on their approach to third-party application patching, key pros and cons, and wrap up with real-world scenarios we encounter in our conversations with the Recast community. 

Core Features: Similarities and Differences 

Both Intune and ConfigMgr help deploy software, enforce configurations, and ensure compliance on managed devices. They can also be used together in a co-management setup, letting you enjoy the benefits of cloud-based management while retaining on-premises control. 

Deployment Model and Infrastructure 

• Intune: Intune is a cloud-based service that requires no local servers. This makes it a great fit for remote users and BYOD (Bring Your Own Device) scenarios. Its web portal offers a modern, simplified management experience. 
• ConfigMgr: ConfigMgr is an on-premises solution that requires server infrastructure—site servers, databases, and client agents. This model works best for organizations with a robust on-premises network and offers detailed control over every patch. 

Application Patching Mechanism 

• Intune: Intune uses Windows Update for Business (WUfB) to manage Windows OS updates. The process is designed to be “set it and forget it,” where updates are automatically applied based on defined deferral policies. This model favors ease of use but offers less granular control over individual updates. 
• ConfigMgr: ConfigMgr leverages Windows Server Update Services (WSUS) to give administrators full control over update approval, scheduling, and deployment. You can carefully select which patches to push to which devices, making it ideal for environments that require detailed testing before full deployment. 

Third-Party Application Patching 

• Intune: Traditionally, Intune has not provided native support for patching third-party applications. Instead, administrators have had to rely on workarounds—such as repackaging app updates as Win32 apps, deploying Microsoft Store apps, or using custom scripts (e.g., with the Winget package manager). Microsoft is actively working on improvements, including introducing Enterprise Application Management in Intune, which aims to simplify updates for certain third-party applications. 
• ConfigMgr: ConfigMgr can subscribe to third-party update catalogs from vendors like Adobe, Oracle, and Dell. These catalogs allow ConfigMgr to manage and deploy third-party patches through its familiar Software Updates workflow. Although the process isn’t completely hands-off—manual intervention may be required for apps without an available catalog— ConfigMgr offers a more integrated solution for managing a broad range of third-party updates. 

Pros and Cons at a Glance 

Intune 

Pros: 

• Cloud-Based Convenience: No need for on-premises infrastructure simplifies management, especially for organizations with remote or mobile workforces. 
• Ease of Use: Intune’s web-based console is modern and easy to navigate, striving to make routine tasks simple for IT teams. 
• Modern Update Process: Automated update rings and Windows Autopatch reduce the workload of keeping Windows and Microsoft apps up to date. 

Cons: 

• Limited Third-Party Patching: Without native support for third-party updates, you must use alternative methods such as custom packaging or third-party tools. 
• Less Granular Control: While automation is beneficial, the inability to selectively approve specific patches might be a drawback in environments that require strict testing and scheduling. 
• No Server Management: Intune does not support patching Windows Servers, which can be a critical gap for mixed IT environments. 
• Dependence on Internet: Devices must have reliable internet access, which can be challenging—or even impossible—in highly secure or isolated networks. 

ConfigMgr 

Pros: 

• Granular Control: Offers detailed management of patch approval, scheduling, and deployment, essential for environments with strict testing or compliance needs. 
• Integrated Third-Party Support: Native integration with third-party update catalogs means many common applications can be patched through the same process as Windows updates. 
• Handles Complex Environments: Ideal for large enterprises with thousands of endpoints, including servers and legacy systems. 
• Detailed Reporting: Robust reporting capabilities help in tracking patch compliance and meeting auditing requirements. 
• Extensible and Mature: A longstanding solution with deep integrations and support for co-management with Intune. 

Cons: 

• Infrastructure and Complexity: Requires significant on-premises infrastructure and a higher level of IT expertise, which can be a barrier for smaller organizations. 
• Steep Learning Curve: Managing ConfigMgr effectively demands a solid understanding of its many features, from site hierarchies to WSUS integration. 
• Less Suitable for Mobile and Remote Devices: While ConfigMgr can manage remote devices via VPN or cloud management gateways, it isn’t as seamless as Intune’s cloud-first approach. 
• Limited Modern Platform Support: ConfigMgr is primarily focused on Windows, with limited support for non-Windows endpoints compared to Intune. 

Real-World Use Cases 

Small to Mid-Sized Organizations 

We find that for companies with a few hundred users, especially those that are cloud-first or have a remote workforce, Intune is often the better fit. Its ease of use, low infrastructure overhead, scaling agility, and integration with cloud services make it ideal for quickly deploying updates to Windows 10/11 devices and mobile endpoints. For third-party app management, supplementing Intune with auto-patching solutions can bridge the gap. 

Large Enterprises with Complex Environments 

We work with many organizations with thousands of endpoints, environments that often include servers and specialized applications. Most continue to see significant benefits from ConfigMgr (you can explore some of their experiences here). ConfigMgr’s granular control not only allows IT teams to thoroughly test patches before deployment but also provides a high level of customization in app deployment, giving you full control over both the timing and method of deployment. This flexibility is a huge advantage for larger organizations that need to tailor rollout strategies to meet complex operational demands. Additionally, ConfigMgr’s native support for third-party updates through vendor catalogs, along with its detailed reporting, is critical for industries with strict compliance requirements—such as banking or healthcare. 

Hybrid Environments 

Many organizations find that a hybrid approach works best. By co-managing endpoints with both Intune and ConfigMgr, you can leverage the strengths of each platform. For example, use Intune to manage remote, mobile, or Windows 11 endpoints, while ConfigMgr continues managing server patches and devices needing granular update control. This balance allows you to transition gradually to a cloud-first model without sacrificing the capabilities needed for legacy systems. 

Conclusion 

Deciding between Intune and ConfigMgr for third-party application patching depends on your organization’s size, infrastructure, and specific patching needs. Intune offers simplicity and cost-effective cloud management ideal for remote and modern environments, but it requires additional solutions to handle third-party updates comprehensively. In contrast, ConfigMgr provides a robust, controlled environment for patching a wide range of applications, including third-party software, but it comes with higher infrastructure demands and complexity. 

Ultimately, many organizations find that a hybrid approach—leveraging the strengths of both platforms—provides the best balance of agility and control. Assess your environment’s needs and resources to choose the right tool or mix of tools to ensure your systems stay secure and up to date. 

Find additional third-party application management and patching posts here.