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Click Edit > Settings.
For example, C:\Program Files\FileZilla Server\your _domain_name.key
For example, C:\Program Files\FileZilla Server\your _domain_name.pem
On the first connection using the FileZilla client, you are presented with the certificate files from the server.
To avoid receiving this prompt on future connections, in the Unknown certificate window, check Always trust certificate in future sessions, and then click OK.