Apple - Where are my iBooks stored in macOS?

If you’ve enabled iCloud, they’re stored in Mobile Documents folder.

Here’s the full path to books you've added:

~/Library/Mobile Documents/iCloud~com~apple~iBooks/Documents/

Here's the full path to books purchased through the iBooks store:

~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks

The path is only accessible via Terminal. Going through Finder will only redirect you to the iCloud folder. So open up Terminal:

For books you've added type in:

open ~/Library/Mobile\ Documents/iCloud\~com\~apple\~iBooks/Documents

For books you've bought on the iBooks store type in:

open ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks

This will open a Finder window with your iBooks in it.

I simply dragged the books onto a folder of my choice in Finder and got the epub files that way.

/Users/USERNAME/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks

This worked for me in Sierra.