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I'd like to setup two different FTP accounts with different physical paths. For instance, if you log on with user A, its working directory will be in E:\UserA and if you log on with user B, its working directory will be in E:\UserB.

Right now, the FTP server is set up so that it has a single user with a single physical path set.

I can always just host a second FTP server that points to a different physical path, but I'd like to save the trouble and just work with a single FTP server if possible.

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You can do this with FTP User Isolation
Choose for the option "Do not isolate users. Start usirs in User name directory"
Make sure you have the needed folders in your FTP root folder

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