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Configuration Manager Patch Management Guide

by Lauren Ballejos, IT Editorial Expert
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Instant Summary

This NinjaOne blog post offers a comprehensive basic CMD commands list and deep dive into Windows commands with over 70 essential cmd commands for both beginners and advanced users. It explains practical command prompt commands for file management, directory navigation, network troubleshooting, disk operations, and automation with real examples to improve productivity. Whether you’re learning foundational cmd commands or mastering advanced Windows CLI tools, this guide helps you use the Command Prompt more effectively.

Key Points

  • Configuration Manager (ConfigMgr), formerly SCCM, is now part of the Microsoft Intune suite but maintains its own development and release schedule.
  • Configuration Manager excels in on-premises control, granular patching, and advanced reporting, while Intune is better suited for cloud-native workloads and mobile device management.
  • ConfigMgr is ideal for large enterprises and MSPs managing complex Windows environments, but not for small teams or those needing cross-platform support.

Configuration Manager (ConfigMgr), formerly System Center Configuration Manager (SCCM), is now integrated into the Microsoft Intune suite. While the software continues to receive its own development and release schedules, some functionalities and workloads have been shifted to Intune.

This guide offers a quick overview of how Configuration Manager can optimize patch management strategies.

What is Configuration Manager?

Configuration Manager can automate the following steps in the patching process: asset discovery, assessment, and deployment. It’s typically considered an on-premise solution, though it also has important capabilities for managing remote endpoints.

As you may suspect, however, Microsoft Intune covers for what the former lacks when it comes to cloud-native workloads. Conversely, Configuration Manager may be necessary to account for what Intune lacks in complex and hybrid enterprise environments.

Configuration Manager at a glance

The table below highlights the core functionalities and practical applications of Configuration Manager. See if the software’s capabilities align with your organizational needs.

CategoryDetails
Core definitionA centralized endpoint management solution from Microsoft, now part of the Microsoft Intune suite.
Use casesPatch management, software deployment, OS imaging, endpoint protection, compliance reporting, and hardware/software inventory for Windows-based environments.
Why it mattersEnsures systems are secure, compliant, and up to date with automated patching and centralized control. Supports hybrid environments and integrates with Microsoft Intune for cloud-based management.
Common mistakesOverlooking prerequisite checks before deployment, not testing updates in a staging environment, misconfiguring Automatic Deployment Rules (ADRs), and failing to maintain an up-to-date inventory of assets.
Best forLarge enterprises, MSPs, and IT teams managing Windows environments who need granular control, on-premises capabilities, and advanced reporting.
Not ideal forSmall businesses with limited IT resources, teams needing cross-platform support (macOS, Linux), or those seeking a purely cloud-based solution without on-premises requirements.

In summary, Configuration Manager, much like Intune, is designed for endpoint management. However, they excel in different scenarios. While ConfigMgr thrives in on-premises control and advanced patching workflows, Intune shines with cloud-native scalability and mobile device management.

Patch management capabilities of Configuration Manager

The capabilities of Configuration Manager go beyond basic update distribution, offering granular control, reporting, and integration with broader IT management workflows. Here’s a look at its core management features:

Automated update synchronization

Configuration Manager can automate patch management cycles by synchronizing updates directly with Microsoft Update and third-party catalogs. Patches can then be classified by severity, product, and applicability, reducing manual effort and common errors.

This automation reduces the risk of vulnerabilities and compliance gaps, streamlining the process of keeping systems up to date.

Dynamic device collections

Devices can be organized into dynamic collections based on criteria (e.g., department, operating system, risk level) using Configuration Manager, allowing tailored patching schedules and targeted deployments.

Third-party patch support

Beyond Microsoft products, Configuration Manager extends patching to third-party applications like Adobe, Java, and Chrome using vendor-specific update catalogs or partner solutions. This broader coverage addresses vulnerabilities in non-Microsoft software, strengthening an organization’s overall security posture.

Automatic deployment rules (ADRs)

ADRs automate the patching process by allowing IT teams to define schedules, criteria, and exclusions, such as excluding non-critical updates. This automation streamlines routine tasks, reduces manual workload, and ensures consistency across large-scale environments.

Maintenance windows

Configuration Manager allows administrators to schedule updates during off-peak hours or predefined maintenance windows. This scheduling minimizes disruption to business operations, ensuring updates are applied when they have the least impact on productivity.

Create a robust patch management strategy

If your focus is security, compliance, and deep Windows endpoint management, Configuration Manager is a strong choice to manage your fleet. For end-to-end IT operations, multi-platform support, or cloud-first strategies, an RMM platform may better complement. To learn more, see our featured blog on Autonomous Patch Management.

Related topics:

FAQs

Yes. SCCM and Microsoft Configuration Manager refer to the same tool. The name change aligns the product with the Microsoft Intune suite.

Configuration Manager is included in the following plans: Intune user subscription license (USL), EMS E3, EMS E5, Microsoft 365 E3, Microsoft 365 E5, and Microsoft 365 F3 (formerly Microsoft 365 F1).

Configuration Manager integrates with Microsoft Intune through co-management, allowing organizations to combine on-premises control with cloud-based management.

Yes. Many MSPs use Configuration Manager for Windows patching and compliance, while leveraging an RMM tool for broader IT operations, monitoring, and cross-platform support.

You risk security vulnerabilities, compliance gaps, and feature limitations, especially as Microsoft phases out support for older versions.

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