It depends on your setup.

If you have a separate home partition then you choose a custom
installation. Format root and choose mount point as / and with home you
choose to use that partition and set the mount point as /home, but do NOT
format. Double check before moving on that the only partition set to format
is /. I have done this a hundred times or more. It works.

If you have everything together on one partition then the only option is to
backup home to an external device, including hidden files and folders.
Format everything and copy over home with the backed up data.