How to uninstall SCCM2012 Secondary Site manually

I wanted to remove a Secondary Site so that I can rebuild it. There were two options, Uninstall or Delete. I chose Delete.

Guess what, my Secondary Site is now removed from the Primary Site. I tried to reinstall Secondary Site on the same computer which I have setup the Secondary Site. I was greeted with “A site server or site system role is already installed on the computer selected for secondary site installation. Remove the site or site system role from the computer, or select another computer for secondary site installation.”

Bumber… Deleting Secondary Site!= Uninstalling Secondary Site. It only removes the Secondary Site from the Primary Site and the Secondary Site components are still installed on the Secondary Site.

I checked Program and Features in my ex Secondary Server, indeed there is a Microsoft Configuration System 2012 Secondary Site installed there. I read online, I only can remove it through the SCCM Primary Site, now what?

I ran to uninstall the Microsoft Configuration System 2012 Secondary Site program, no avail.  The computer doesn’t seem to be doing anything. I only saw a SETUP.EXE running and it’s not doing anything at all. I was hoping the CPU usage would jump even 1% or 5%. Nope. Deleting entries from registry is too hard.

Found a way to uninstall the Secondary Site manually on the Secondary Site itself

1. Run CMD as elevated C:\Program Files\Microsoft Configuration Manager\bin\X64\SETUP /DEINSTALL (x86 if you are 32bit)
2. Once you see the command prompt line stating something like Microsoft SQL Server 2008, the computer has started to do its job.
3. Check the Program and Features, voila! It’s gone!

I am currently reinstalling my Secondary Site and cleared the prerequisites, no more errors. I do not have my Win2k8R2 CD with me… reinstalling Windows Server is not going to be an option.

Hope this helps!



10 thoughts on “How to uninstall SCCM2012 Secondary Site manually

  1. Tomas says:

    Thank you. I have been banging my head for hours because I too deleted the site!

  2. Jaco says:

    Hi, this location does not exist on my secondary site. C:\Program Files\Microsoft Configuration Manager\bin\X64\
    Any idea why not and how I can manually uninstall?

  3. Jaco says:

    Windows Server 2008 R2 64-bit. I looked under Program Files and Program Files x86 but that path just does not exist.

    • Phyllis says:

      Hi again Jaco,
      1. Was the Secondary Site installed successfully?
      2. Possible to check to see if there is any System Center Secondary Site components installed under Program and Features?

      Please let me know 🙂

  4. A says:

    I just uninstalled Secondary site manually through add and remove program uninstall option and it uninstalled the secondary server

  5. […] I then found this fantastic blog post that Phyllis in IT has written: How to uninstall SCCM2012 Secondary Site manually. […]

  6. Bryan Gonzalez says:

    +1 Google led me here

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