Let’s Encrypt offers Domain Validation (DV) certificates.
Does Let’s Encrypt issue certificates for anything other than SSL/TLS for websites?
"Let’s Encrypt certificates are standard Domain Validation certificates, so you can use them for any server that uses a domain name, like web servers, mail servers, FTP servers, and many more.
Email encryption and code signing require a different type of certificate that Let’s Encrypt does not issue."
There is the DNS-01 challenge of the Challenge Types - Let's Encrypt that might work well for you.
And here is a list of DNS providers who easily integrate with Let's Encrypt DNS validation