Hello @brendan
Please note that we usually recommend to use separate clean server for Document server installation. It’s necessary to avoid dependency and port conflicts. But if you prefer docker installation, there’s all-in-one guide for Nextcloud+ONLYOFFICE:
As for the issue in general, if Nextcloud uses 80 port you won’t get LE certificates, since certbot uses 80 port for first validation. We discussed it earlier here:Install OnlyOffice docker with Https on a different port does not work
Do I understand you right that you have a proxy-server in front of your server?