To be sure it should create 3 files the database, private and the public files. If that is the case your good and assuming all your customized apps are using version control like git
@ccfiel This is the part I keep missing. So any changes made to the file system need to be committed to git? For instance, JSON files in the individual docs folders will not be backed up with bench?
Yes it should be and bench update task is git pull from frappe framework source, erpnext if it’s installed and all other 3rd party apps installed in your site.
Shouldn’t we also backup site_config.json, or at least copy some of it’s content to new site, i.e. SSL certificate & key location, Dropbox API key etc?