We would like to set up a Document Library in a SharePoint Online site with different members, visitors and owners than the Site the Document Library will be created in. It works very well (we have different population for visitors [read] and "members" ) but we can't prevent parent Site Owner's from having ~Full Control access to the Library even if they do not have explicit Full Control permission on (they are not owner of) the Library. Please note: These owners are NOT Sites Collection Administrators (which, we know, cannot be denied access to a library). Thanks, Pierre
Yes, You can deny a Site owner (Not a Site Collection Admin) to have access to one document library. You can achieve this by breaking the permission inheritence for that particular library. go to
Library Settings --> Permission for this document library --> Stop Inheritence permission --> After this select the checkbox Site owner group and click on Remove user permission. and Done
Please note: you can not restrict the site collection admin to access this document library even after performing above steps.
Edit1: As suggested by Derek, you have put the user in a different custom site owner group with a custom permission level where the "Manage Permission" is not available for the person. Know More on SP Permission Level