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Traditionally control of files server has been with Windows administrators in my organization and applications are managed by application administrators.
Now we are implementing Sharepoint, and all documents to be migrated to SP.
If i understand correctly , A site collection admin will automatically have access to the document library.
Is it possible that I have a separate admin for document libraries and application.
This is highly impossible . Because the SharePoint admin will always have full access to the document libraries.
There is a non sharepoint way though ,although this may seem weird but you can password protect the documents if the privacy of documents is that important to you.
Agree with Yash.kamdar and Mike Smith. The only option could be to create separate Site Collections for the various types of confidential documentation, and assign the Site Collection ownership to very specific users. Then only those people and those with access to the SharePoint Admin account or Global O365 admin account will have access to the documents
Short answer, No. A Site Collection Administrator cannot be blocked from any content in their Site Collection.
