Short answer: in the SCCM vs WSUS vs Intune comparison, each tool does a different job. Configuration Manager (SCCM) is an on-premises suite for managing servers, desktops and laptops. WSUS is a free Windows update server that Microsoft has deprecated. Intune is a cloud service for user devices, while Microsoft points servers to Azure Update Manager, which needs Azure Arc for on-prem machines.
This guide compares all four, plus JetPatch, from the point of view of a server and infrastructure team. It covers what each tool is built for, how it handles on-prem and air-gapped servers, and whether it can patch Linux and Unix. If you have already decided to move server patching off ConfigMgr, read our guide to choosing an SCCM alternative for servers instead.
SCCM vs WSUS vs Intune vs Azure Update Manager at a glance
The table summarizes each tool as Microsoft documents it today. Cost is described qualitatively, because licensing depends on your agreement.
| Tool | Built for | Servers or endpoints | On-prem / air-gapped | Linux and Unix | Cost model |
|---|---|---|---|---|---|
| SCCM / ConfigMgr | Deploying apps, software updates and operating systems; compliance settings | Both: servers, desktops and laptops | On-prem by design; isolated sites need extra site design and manual content steps | Linux and UNIX clients removed in version 1902 | Microsoft licensing plus your own SQL Server and site infrastructure |
| WSUS | Approving and distributing Microsoft updates | Both, Windows only | On-prem; disconnected setups rely on manual export and import | None | Included as a Windows Server role; you run and maintain the servers |
| Intune | Cloud management of devices and apps (MDM and MAM) | Endpoints: Windows client, macOS, mobile and some Linux desktops | Cloud only; no on-prem infrastructure | Ubuntu and RHEL devices; no AIX or Solaris | Per-user or per-device subscription |
| Azure Update Manager | Update assessment and scheduling for server operating systems | Servers; not Windows 10 or 11 | Azure VMs natively; on-prem servers only through Azure Arc | Windows and Linux; no AIX or Solaris | No extra charge for Azure VMs; most Arc-enabled servers billed per server per month |
| JetPatch | Server patch management with governance and audit reporting | Servers first, plus Windows endpoints | Installed on your infrastructure; connected, restricted or fully air-gapped | RHEL, Ubuntu, SUSE and other Linux; IBM AIX and Oracle Solaris | Commercial licence; no Azure tenant required |
What changed: WSUS is deprecated
In September 2024 Microsoft announced that WSUS is deprecated. Microsoft’s list of features no longer in development now says WSUS “is no longer actively developed” and that all existing capabilities and content remain available.
Deprecated does not mean removed. WSUS still ships with Windows Server and keeps working. But it will not gain new features, and Microsoft’s direction is clear: Intune and Windows Autopatch for client devices, and Azure Update Manager for servers. Microsoft also said the deprecation does not change existing Configuration Manager capabilities, which still use WSUS underneath.
For server teams, that turns an old “SCCM vs WSUS” question into a wider one: where should Windows Server patching live for the next five years? Our overview of WSUS deprecation options for Windows servers walks through the four realistic paths.
Microsoft Configuration Manager (SCCM)
System Center Configuration Manager is now called Microsoft Configuration Manager, and many teams still say SCCM or ConfigMgr. Microsoft describes it as part of the Microsoft Intune family of products. It covers deployment of applications, software updates and operating systems, compliance settings, and management of servers, desktops and laptops. It remains a supported, current-branch product.
Patching is one feature inside that suite. ConfigMgr integrates with WSUS to manage software updates, and relies on SQL Server, IIS-based site system roles and Active Directory. Microsoft itself advises careful planning and testing, because the product can affect every computer in an organization.
- Strengths: deep Windows control, task sequences, maintenance windows, asset inventory, detailed reporting and OS deployment. It fits well when you already use the whole suite.
- Infrastructure: site servers, a SQL Server database, management points and distribution points that your team must run and upgrade.
- Platform limits: Microsoft’s deprecated client list shows Linux and UNIX client support removed in version 1902, and macOS client support removed at the end of 2022.
- Co-management: ConfigMgr can be paired with Intune, which helps desktop teams but adds configuration to watch.
WSUS (Windows Server Update Services)
WSUS is a dedicated update server. It downloads Microsoft updates once, lets you approve them by computer group, and distributes them across your network. It is included as a Windows Server role, which is why so many server estates still depend on it.
- What it does well: saves bandwidth, scales to large Windows estates and keeps update content on your own network. It also sits underneath ConfigMgr and many other tools.
- Where it falls short: basic scheduling and reporting, no orchestration of maintenance windows or staged rollouts, and maintenance work such as database cleanup.
- Coverage: Microsoft products only. Third-party application updates need extra catalog tooling, and there is no Linux or Unix support.
- Isolated networks: a disconnected WSUS fed by manual export and import works, but it is slow and hard to evidence for auditors.
Microsoft Intune
Microsoft describes Intune as a cloud-based endpoint management service that runs entirely in the cloud, with no on-premises infrastructure. It manages devices (MDM), apps and app data (MAM), and feeds device compliance into Microsoft Entra Conditional Access. Windows updates are controlled through policies such as update rings, while the devices pull updates from Microsoft.
Intune is a strong choice for laptops, desktops, BYOD and remote workers. It is a weaker fit for data-center servers. Microsoft’s supported platforms list names Windows client editions, macOS, iOS, Android, Chrome OS and some Linux (Ubuntu and RHEL 9 and 10). Windows Server is not on that list, and neither are AIX or Solaris.
- Strengths: no servers to run, policy-based compliance, Zero Trust integration and good support for distributed users.
- Limits for server teams: devices must reach Microsoft’s cloud, so isolated networks are out of scope, and production change windows and approvals are not what it was designed around.
- Cost: each managed user or device needs an Intune license.
Azure Update Manager: Microsoft’s answer for servers
Azure Update Manager is the Microsoft service positioned for server updates. It assesses and schedules Windows and Linux operating system updates. Its FAQ is direct: machines that are not running on Azure must be enabled for Azure Arc to be managed by Update Manager.
- Pricing: no extra charge for Azure VMs. Other Arc-enabled servers are charged per server per month, prorated daily, with exceptions such as servers covered by Software Assurance or Defender for Servers Plan 2.
- WSUS as a source: you can point the Windows Update client at WSUS and let Update Manager handle schedules, but each server still needs Arc.
- Scope: it does not patch Windows 10 or 11; Microsoft recommends Intune for those.
For teams standardized on Azure, it can be the shortest path. For air-gapped sites, data-sovereignty rules or large non-Azure estates, Arc adds a cloud dependency that may not be acceptable.
SCCM vs Intune: which fits which job
The “Intune vs SCCM” decision is mostly about device type and infrastructure. Microsoft now sells them as one family, and many organizations run both through co-management.
| Scenario | Better fit | Why |
|---|---|---|
| On-prem Windows servers with strict change windows | SCCM (or a server-focused tool) | Maintenance windows, deep OS control, works on your network |
| Remote and hybrid workers | Intune | Devices managed over the internet with no VPN or site servers |
| BYOD phones and tablets | Intune | App protection without owning the whole device |
| OS deployment and app packaging for desktops | SCCM | Task sequences and mature content distribution |
| Microsoft 365 and Entra-centric organization | Intune | Built-in Conditional Access and identity integration |
| Gradual move from on-prem to cloud for desktops | Both (co-management) | Shift workloads one at a time |
| Mixed Windows, Linux and Unix servers | Neither on its own | Neither manages AIX or Solaris; SCCM no longer has a Linux client |
WSUS vs SCCM: what you actually gain
SCCM does not replace WSUS. It uses a WSUS-based software update point and adds deployment, scheduling, maintenance windows and reporting on top. So the “WSUS vs SCCM” choice is really about whether you need that management layer, and whether you want to run the infrastructure that comes with it.
- WSUS alone suits a small, Windows-only estate where an admin approves updates and Group Policy handles installs.
- SCCM suits large Windows estates that also need app and OS deployment.
- A patch management platform on top of WSUS suits server teams that need governance, readiness checks and audit reports, without the full ConfigMgr suite, and often for Linux and Unix too.
The gap: Linux, Unix and isolated servers
Most enterprise server estates are not Windows-only. RHEL, Ubuntu and SUSE run alongside Windows Server, and energy, finance, telecom and government estates often still run IBM AIX or Oracle Solaris. Many of those servers sit in restricted or fully air-gapped segments.
That is where the Microsoft toolset thins out. WSUS is Windows-only. ConfigMgr dropped its Linux and UNIX client. Intune’s Linux support targets desktops, and it needs the cloud. Azure Update Manager handles Linux, but only through Arc for on-prem machines, and it does not cover AIX or Solaris. Teams end up with one tool for Windows, another for Linux, and scripts and spreadsheets for Unix, which means three processes and three sets of audit evidence.
How to choose for a server estate
Answer these questions before you pick a tool:
- Can these servers reach the internet? If some sites are air-gapped, cloud-only tools are ruled out for them.
- Where must patch data live? Regulated teams often need approvals and inventory to stay on their own network.
- Are you standardized on Azure? If yes, Azure Update Manager may be the shortest path. If not, Arc is a new dependency.
- How mixed is the estate? Count Linux, AIX and Solaris servers, not just Windows.
- What do you use SCCM for? If it runs only server updates, you are carrying a full suite for one job.
- What is your WSUS plan? Decide whether to keep WSUS for now, replace it, or do one and then the other.
How JetPatch helps
JetPatch is installed software that runs on your own infrastructure, on-premises or in your private cloud tenancy. No Azure tenant, Azure Arc or vendor-hosted service is required. It patches Windows Server, Linux, IBM AIX and Oracle Solaris from one console.
- Keep WSUS or replace it. JetPatch integrates deeply with your existing WSUS, including primary and replica servers, bidirectional group sync and third-party application patching through the WSUS pipeline. Or it replaces WSUS with the JetPatch repository. You can start in WSUS mode and switch groups when your change calendar allows. See the WSUS replacement options.
- Air-gapped servers. Offline Windows Patching brings digitally verified updates to isolated servers without giving them internet access. Local Linux repositories serve isolated Linux servers.
- Linux and Unix in the same console. Advisory-level patching (RHSA, RHBA, RHEA) with CVE correlation for Enterprise Linux, AIX through NIM and SUMA, and Solaris through IPS and CPU repositories.
- Governed rollouts. Endpoint Readiness and Predictive Patching find blockers before the window. Sequence Patching moves updates from QA to staging to production, and deployments can wait for ServiceNow or Jira approval.
- Audit evidence. Compliance reports by OS, environment and remediation plan, exported to CSV and PDF.
JetPatch does not have to replace ConfigMgr or Intune for desktops. Many teams keep those for user devices and move server patching to one server-focused console. The Windows patch management page covers supported Windows Server versions and both WSUS modes.
FAQ
What is the difference between SCCM, WSUS and Intune?
WSUS is a Windows update server that downloads and distributes Microsoft updates on your network. SCCM (Configuration Manager) is an on-premises management suite that uses WSUS for updates and adds app deployment, OS deployment, scheduling and reporting. Intune is a cloud service for managing user devices and apps, with no on-premises infrastructure.
Is Intune replacing SCCM?
Not formally. Configuration Manager is still a supported product and is now part of the Microsoft Intune family, and the two can run together through co-management. Many organizations are moving desktop workloads to Intune, but Intune is built for user devices and does not list Windows Server as a supported platform.
Is WSUS being discontinued?
Microsoft announced in September 2024 that WSUS is deprecated, meaning it is no longer actively developed. It still ships with Windows Server and existing capabilities remain available. It will not get new features, so most server teams are planning their next step now.
What replaces WSUS for on-premises servers?
Microsoft points servers to Azure Update Manager, which manages on-prem machines only through Azure Arc, usually with a per-server monthly charge. Teams that need patching to stay on their own network use an on-prem platform. JetPatch can keep working with your WSUS or replace it with the JetPatch repository, including for air-gapped servers.
Can SCCM or Intune patch Linux and Unix servers?
Configuration Manager removed Linux and UNIX client support in version 1902. Intune supports some Ubuntu and RHEL devices but is aimed at desktops, and neither tool covers AIX or Solaris. JetPatch patches Linux, AIX and Solaris servers from the same console as Windows Server.
Can I keep SCCM for desktops and use another tool for servers?
Yes. Many teams keep ConfigMgr or Intune for user devices and move server patching to a server-focused platform. Make sure each server is targeted by only one patching tool to avoid double deployments.
Want to see how your servers would run with or without WSUS, on-prem or air-gapped? Request an evaluation and compare JetPatch with your current Microsoft tooling on a pilot group.
