Once you’ve setup a Let’s Encrypt certificate on your MikroTik RouterOS or CHR router, you can configure the API service to use it.
Login to your router using ssh, e.g. ssh [email protected].
Now copy-and-paste the following:
/ip/service set api-ssl certificate=[/certificate find where name~"^letsencrypt.*"]
This has been tested only in the circumstance that one letsencrypt certificate exists. I will update this post once I get around to testing it with multiple (renewed) certificates.