In-place OS upgrade for SCCM site server

Jonathan LefebvreSCCM20 Comments

The latest releases of SCCM Current Branch(1702 and 1706) bring a new round of requirements. With SCCM 1702, it’s required to run site servers on a Windows Server higher than 2008 R2. Now with SCCM 1706, some of the new features like Manage Microsoft Surface driver updates, requires that all Software Update Point (WSUS) runs on Windows Server 2016. We can assume that we’ll see more of those new features requiring Windows Server 2016 in the future.

In this post, we will detail how to do an in-place OS upgrade from Windows Server 2012 R2 to Windows Server 2016, on an SCCM primary site with SQL installed locally.


  • SCCM Current branch minimum level 1602
    • See our latest post to upgrade SCCM to 1706 here
  • Minimum versions for SQL server, if installed on the site server :
    • 2012 SP2 and up
    • 2014 SP1 and up
    • 2016 RTM and up
    • See KB here for more details

Tasks before In-place OS upgrade

  • Install all the latest Windows updates, as the Upgrade setup will ask for it.

In-place OS upgrade SCCM server

  • Uninstall System Center Endpoint Protection client, if used.

In-place OS upgrade SCCM server

This is needed as Windows Server 2016 as Windows Defender built-in. As per Microsoft documentation, not removing SCEP client, could prevent the upgrade. Also, consider validating your Antivirus solution recommended approach with in-place OS Upgrade
With previous in-place OS upgrade from Windows Server 2008 R2 to Windows Server 2012/R2, it was required to removed WSUS. This was due to a WSUS version change. This is no longer required, as Windows Server 2012/R2 and Windows Server 2016 uses the same WSUS version.


In-place OS upgrade SCCM server

  • Insert/Mount the Windows Server 2016 media and Start Setup.exe

In-place OS upgrade SCCM server

  • Select Download and install updates and click Next

In-place OS upgrade SCCM server

  • If there are still update, the setup will let you know

In-place OS upgrade SCCM server

  • Enter Product key, click Next

In-place OS upgrade SCCM server

  • Select Windows Server 2016 (Desktop Experience)

In-place OS upgrade SCCM server

[su_box title=”Note” style=”glass” title_color=”#F0F0F0″]Windows Server Core is not supported for Site server. [/su_box]
  • Accept license terms

In-place OS upgrade SCCM server

  • Select Keep personal files and apps, click Next

In-place OS upgrade SCCM server

  • Gettings updates if still needed

In-place OS upgrade SCCM server

  • Validating before upgrade

In-place OS upgrade SCCM server

  • Warning about Windows Server upgrades. SCCM support it, so click Confirm

In-place OS upgrade SCCM server

  • Validating available space on C:\ drive

In-place OS upgrade SCCM server

  • If there is not enough space, you will receive the following screen. Otherwise, it will show that it is ready, click Refresh

In-place OS upgrade SCCM server

  • Installation will begin

In-place OS upgrade SCCM server

  • The installation will proceed and automatically reboot.

In-place OS upgrade SCCM server

  • Once completed, the logon screen will display

In-place OS upgrade SCCM server

Post Upgrade tasks

In-place OS upgrade will require post upgrade tasks to be completed. Some services have been set to disable or haven’t started after the initial boot under the new OS.

  • IIS services are stopped and disabled
    • Many SCCM component require IIS, so this needs to be fixed

In-place OS upgrade SCCM server

  • Open the Services management console
  • Browse to World Wide Web Publishing  service, and set it back to Automatic

In-place OS upgrade SCCM server

  • Browse to Windows Process Activation service, and set it back to Automatic

In-place OS upgrade SCCM server

  • SCCM Services are also not running.
    • Rebooting the server after validating they are set to automatic, will correct this situation.

In-place OS upgrade SCCM server

  • Reboot the server
  • If the site server is hosting the WSUS/SUP role, action must be taken, as the WSUS Configuration Manager will return error about the availability of WSUS on the local server

In-place OS upgrade SCCM server

  • To fix this, Launch the Post-Installation tasks of WSUS from the Server Manager
    • Be sure to have fixed the services of IIS/SCCM and rebooted the server prior to run the Post-installation tasks, as WSUS rely on IIS also.

In-place OS upgrade SCCM server

  • One last reboot is needed so WSUS/SUP are correctly configured.
  • Look at the Monitoring/System Status/Component Status if any error remains. Fix them before going any further with SCCM functionally.


In-place OS upgrade SCCM server

Do not forget about Antivirus action after the upgrade. Most probably an update or re-installation will be needed.

If you use System Center Endpoint Protection, it should be reinstalled to manage Windows Defender, just like Windows 10

Click here for more details about In-place OS Upgrade for SCCM servers

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That’s it, you’ve successfully upgraded your server to Windows Server 2016.


Contributor of System Center Dudes. Based in Montreal, Canada, Senior Microsoft SCCM consultant, working in the industry for more than 10 years. He developed a strong knowledge of SCCM and MDT to build automated OS deployment solution for clients, managed large and complexe environment, including Point of Sale (POS) related projects.

20 Comments on “In-place OS upgrade for SCCM site server”

  1. Had issue opening console after upgrade from 2012 r2 TO 2016. Ran mofcomp smsprov.mof and console started working.

  2. Jonathan,

    I’m getting ready to do an in place upgrade of my 2012r2 to 2016. My ConfigMgr version is CB1802. When reading your article you say that removing the SUS role is no longer needed? Can you please confirm?



  3. Tried following your guide upgrading SUP Site system from 2012R2 to 2016 that hosts FSP and WSUS roles with remote SQL (SCCM CB 1706). Run in to issues after upgrade when running WSUS postinstall tasks.

    First got this error:
    System.SystemException: The trust relationship between this workstation and the primary domain failed. No issues on the box itself just the wsus component that had trust relationship issues.

    Rejoined the domain and was able to move further but then got another error when running WSUS postinstall tasks:

    FixSubscriptionCategories failed. Exception: System.Data.SqlClient.SqlException (0x80131904): Cannot open database “SUSDB” requested by the login. The login failed.
    Login failed for user ‘Computername$’.

    Tried cleaning up WSUS install completely on SUP and SQL with complete reinstalls with no luck. MS pointed to article ( and said that we should:

    “Before you upgrade to a different operating system, you must uninstall WSUS from the server. You may keep the SUSDB and reattach it once WSUS is reinstalled. ”

    Ended up getting a new site system for SUP (or could have reinstalled the OS on the box) and all worked afterwards, so it seems like even though it’s not exactly our scenario it is the only solution:
    In this case, the only known corrective measure is to format the hard drive and reinstall Windows Server 2012 R2.

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  8. I had the following issues after the 2012 R2 to 2016 upgrade on the PS Server

    SMS Host Service would not start –
    Removed and reinstalled the SCCM Client on the Primary site server – FIXED

    IIS Worker Process/W3wp.exe taking 100% CPU –
    Ended w3wp.exe task(to free up CPU), Install latest Cumulative Update for Windows Server 2016 – FIXED

  9. I gave this a shot and did an in place upgrade on our site server thats running wds, iis, and wsus. I followed the steps to re enable wsus services and go through the post installation tasks. When I click on the post installation tasks to finish it up, it errors out and disables the W3SVC service. Any ideas?

  10. If you want to eventually go to 2016 v1709, for 2012r2 or older, it’s best to switch to Core. 1709 is core only AND Server 2016 can only be installed as “Desktop Experience” or “Core” and there’s no switching!

    1. Andy Barzyk – that isn’t really relevant though. Server 2016 1709 is a completely different channel so you can’t upgrade from Server 2016 to 2016 1709 anyway, it has to be a clean install. Also, Server 2016 1709 is for two specific scenarios (hence making it core only), so you would never use it for System Center.

  11. Hello Jonathan,
    I am currently running 1606 on Server 2012R2 and although SCCM reports successful patching of our 2016 servers, when actually viewing installed updates on the machine they were not updated since July/August 2017. So we had to go back and run a script to force them to download and install latest updates directly from microsoft. All of the 2008R2, 2012R2 servers show patched and actually have the patches installed. Why might I be getting a false report on 2016 patch status and why might those servers not be getting patches installed?
    My question is really are there any known issues in 1606 or WSUS or SCCM running on 2012R2 that may cause this?
    Outside of this I’m in the process of opening a Premier Support ticket with MS…
    Thank you!

  12. Hi,

    I have 2 servers:-
    1. Windows server 2012 R2 having Domain Controller
    2. Windows server 2012 R2 having SCCM+SQL
    i need to upgrade this windows server 2012 R2 to windows server 2016 using SCCM.
    Can you please elaborate the steps and provide me the better resolution for this.

    Thanks in advance

  13. Jonathan,

    I have a question about this and also another thing.

    Is the process very similar to this guide if you are running System Center Configuration Manager 2012 R2 SP1 on a Windows 2008 R2 OS? I would like to upgrade to 2012 R2 OS before upgrading to the latest branch of SCCM or 1606 version. Note: We are running SCCM as a virtual machine using VMware.

    I saw you guys have a guide for sale for upgrading to SCCM 1511. I was wondering if you guys had a new guide coming out soon or available now for either the current branch or 1607? Also, I’m interested in a in-place upgrade guide. If you guys don’t have any available is there a good step by step guide likes yours that you guys recommend?

    Thank you,
    Have a great day!

    1. HI Mike,

      First thing, in-place OS upgrade for a SCCM site server is only supported from Current Branch v1602 and up.
      You need to upgrade SCCM before thinking about the OS upgrade.

      To upgrade your SCCM 2012 to Current branch, you can follow our post . Same apply for newest version of SCCM.

      You could upgrade your SCCM 2012 to Current Branch v1606, as this is a baseline version.

      We take note for a future guide.

      Hope this help.

  14. I ran into the issue described in the “Known issue for remote Configuration Manager consoles” on the MS docs site. However, when I navigate under Root there is no SMS entry. Have you seen this?

    1. Hi Bryan,

      can you share the link to the MS article ?
      I didn’t had this issue.


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