How to Change where Configuration Files are Stored

FileZilla Server’s service accepts a --config-dir parameter. You can use this parameter when starting the service.

On Windows, to relocate the configuration files in your folder of choice, open a cmd console with Administrator privileges and run the following command.
SC.exe config filezilla-server binpath= "\"<Install folder>"\filezilla-server.exe\" --config-dir \"<Folder of choice>\""

Where <Install folder> is the folder where FileZilla Server was installed into and <Folder of choice> is the absolute path to your folder of choice.

For example, to store the files under FileZilla Server’s installation folder, and FileZilla Server is installed under C:\Program Files\FileZilla Server, the command should be:

SC.exe config filezilla-server binpath= "\"C:\Program Files\FileZilla Server\filezilla-server.exe\" --config-dir \"C:\Program Files\FileZilla Server\""

Quotes and spaces must be entered exactly like that.
On Debian Linux, as root, open in an editor the file /etc/systemd/system/filezilla-server.service and edit the line following the [Service] label, like this:
ExecStart=/opt/filezilla-server/bin/filezilla-server --config-dir <Your directory of choice >Where <Your directory of choice> is the directory where you want to relocate the configuration files.

Then restart the service, with the following command:
sudo systemctl restart filezilla-server
On macOS relocating FileZilla Server configuration files is not recommended, as the installer will overwrite any change.

FileZilla Pro Enterprise Server’s service accepts a –-config-dir parameter. You can use this parameter when starting the service.