What is the Difference Between SCCM and WSUS?

There are a variety of modern patch management tools available today for organizations to choose from, but many people still have questions about legacy solutions.

Quick answer: WSUS (Windows Server Update Services) is a free, Windows-only patch management tool best for small to mid-sized organizations. SCCM (System Center Configuration Manager, now Microsoft Endpoint Configuration Manager) is a paid enterprise solution offering more control over deployment, reporting, and limited third-party patching. Both are on-premises solutions that struggle with hybrid infrastructure and non-Windows systems.

Both are patch management solutions offered by Microsoft, but there are some significant differences between the two. As legacy patch management solutions, WSUS and SCCM do have a lot in common. They are both on-premises solutions that are primarily focused on Windows OS and Microsoft products.

While a majority of the global desktop market share still goes to Windows, there are an increasing number of devices running alternative operating systems. Third-party applications are taking up a larger share of vulnerabilities, and the number of endpoints organizations need to track is ever-increasing.

Simply put, WSUS and SCCM may have their differences, but both patching solutions are trailing behind the modern workplace. WSUS and SCCM have been around for a long time, but it is still important to understand what each platform does and what their limitations are.

WSUS, or Windows Server Update Services, does have a few benefits. For one, it is a free tool installed as a role on Windows Server, which means that organizations of any size can use it. For companies that are not quite large enough for SCCM, WSUS provides some patching automation with no up-front costs.

WSUS is known for its hidden costs, including time spent on troubleshooting the system and the additional expense of having to acquire and use alternative patching tools for non-Windows operating systems and third-party applications.

WSUS is built by Microsoft, so it should not have problems with Windows systems. If configured correctly, WSUS should be able to patch these systems semi-automatically. If your organization's network solely runs on Microsoft infrastructure, WSUS can help minimize the amount of manual labor required for patching.

What are the limitations of WSUS?

Patching with WSUS may be a feasible option for companies that only use Microsoft, but organizations today are increasingly using hybrid infrastructures to meet their needs. This means that relying on WSUS is not going to be enough to maintain regular patching across the entire network.

WSUS will fix vulnerabilities in your Windows OS, but any macOS or Linux devices are going to be left in the dust. WSUS is limited in its ability to handle patching third-party applications, and it also lacks in terms of reporting and network visibility. While WSUS is good at what it does, it is not good for much else.

Applications from third parties, like Adobe and Java, are attractive options for attackers because they are routinely home to a large number of unpatched vulnerabilities. WSUS does include some pathways for patching these products, but they are extremely difficult to configure and the update catalogs can be hard to follow.

SCCM, or System Center Configuration Manager, is a paid patch management solution from Microsoft. SCCM relies on WSUS to check for and apply patches, but offers some more desirable features and gives users more control over how and when patches are deployed.

While SCCM has a few advantages over WSUS and can seem like a more desirable option for larger organizations, there are still several challenges that companies may face when using SCCM for patch management.

What are the benefits of SCCM?

SCCM includes a number of functions that can benefit users:

• More control over patch deployment timing and targeting

• The ability to generate comprehensive reports

• Greater control over Windows machines on your network

• Endpoint protection tools built in

• Better integration with Microsoft products

If configured correctly, SCCM can be an adequate patch management system for organizations predominantly running on Windows. As a Microsoft product itself, SCCM integrates quite well with Windows systems and Microsoft products.

What are the limitations of SCCM?

Patching with SCCM may not be the best option for every organization. Like WSUS, SCCM is limited in its ability to manage non-Windows operating systems and third-party applications. It is a product built for Microsoft first, and everything else is secondary.

Unlike WSUS, SCCM does offer some rudimentary means of managing alternative operating systems as end-clients. It still requires a Windows server to run, and the functionality for non-Windows operating systems is not as good.

Hybrid infrastructure will still require elements of manual patching with SCCM, and third-party application patching is just as limited. While SCCM does provide more support for third-party apps than WSUS, that is not really saying much. Problems with using SCCM to patch third-party applications are a top source of frustration for IT managers.

Given that third-party software can account for up to 76 percent of the vulnerabilities found on the average PC, it is no surprise that better third-party application management is a top request from IT staff.

SCCM is also prohibitively expensive and is usually sold as part of a larger suite of tools. The pricing for SCCM can also be elusive, as endpoints and servers are typically priced separately. It also requires an SQL server to run, leading to high costs for operation and maintenance.

WSUS and SCCM have both been around for a long time, but they are both hindered by their lack of functionality in modern IT environments. Hybrid infrastructures are increasingly common, and many organizations rely on an array of operating systems and third-party applications to meet their needs. Patch management platforms need to keep pace with the trends in technology if they are going to be efficient.

Legacy solutions like WSUS and SCCM make the process of patching hybrid infrastructure far more complicated than it needs to be. With SCCM, patching for macOS and Linux is a tiresome endeavor. With WSUS, it is not even an option.

Relying on these solutions alone for patch management can put undue stress on your IT staff and can require a significant amount of manual labor between dealing with configurations, maintenance, and additional patching software that may be necessary. Legacy options are also often limited in terms of endpoint management.

Modern patch management solutions, like Automox, give users the freedom to patch their entire network from a single interface, regardless of operating system or third-party status.

Legacy patch management options are severely lacking when it comes to managing security updates across multiple platforms. In addition to limited insight into endpoints and patch status, legacy patching solutions are restricted in their ability to handle patching alternative operating systems and third-party applications. For tech professionals, the failures of legacy patching platforms can be a serious burden that ultimately leads to an overly complex, inefficient patch management strategy.

The best patch management protocol is one that is both effective and efficient. Needing multiple programs for maintaining endpoint visibility and deploying security updates for select devices, operating systems, and applications hardly fits that description.

By employing a cross-platform patching solution, organizations can streamline their patch management strategy while also increasing their effectiveness and efficiency.

How fast can attackers weaponize vulnerabilities?

Cross-platform patch management can help your organization perform critical security updates across your entire network as soon as possible. With full endpoint visibility, a solution like Automox allows IT staff to detect and remediate unresolved vulnerabilities in real time.

While many organizations believe that time is on their side, research from 2025 shows that attackers can weaponize a critical vulnerability in as little as 24 to 48 hours. Currently, it takes organizations an average of 60 to 90 days to patch a critical vulnerability.

The cost of delayed patching continues to climb. In 2024 alone, organizations experienced an average breach cost of $4.88 million according to IBM's Cost of a Data Breach Report. Many of these breaches exploited known, unpatched vulnerabilities.

Overly complex patch management solutions that are difficult to configure and are not compatible with hybrid infrastructure are, in their own right, an impediment to overall cybersecurity. While there may be a slight difference between WSUS and SCCM, these platforms are not different enough to meet the needs of modern IT environments. A cloud-based, cross-platform patching solution that can manage updates for your entire network is crucial to cybersecurity efficiency and effective patch management.

One of the most attractive benefits of cloud-based patching platforms is the lack of necessary upkeep. On-premises, legacy patching solutions often require dedicated servers and routine maintenance, both of which can be costly.

Conversely, cloud-native patching solutions require no maintenance efforts from the end-user. Instead, the platform updates and maintains itself. Cloud-based patching platforms are typically going to be more budget-friendly, largely thanks to the decreased costs associated with operation and maintenance.

How do cloud-native solutions handle remote devices?

Cloud-based patching platforms like Automox also do not rely on a VPN for patching remote devices. The advent of SaaS programs means that many remote workers have no need to connect with a VPN to access company programs and information.

This lack of VPN usage can be an issue for legacy, on-premises patch management solutions. Cloud-native patching options like Automox feature an agent that can be remotely installed on every device or workstation that will deploy necessary patches, no matter the location.

With cloud-native, cross-platform, automated patching solutions on the table, the difference between WSUS and SCCM surely pales in comparison. While WSUS or SCCM may work for some organizations, they are ultimately very similar and share many of the same limitations in the modern workplace. For efficient and effective patch management, organizations need a solution that can fit any IT environment.