The HAProxy hint did the trick. For others searching, here is what I did on HAProxy config:
Defined a specific
backend pointing on 127.0.0.1 with the port defined on ACME config
On the
frontend added an
ACL to forward the requests for which
path starts with /.well-know/... onto the previous backend
Seems to work fine.
Don't hesitate to suggest any improvement though.
In another hand I saw that it could be a small security breach, but I don't see the issue, I'd be interested to know.
Thanks for the help.