Let’s Encrypt has supported Internationalized Domain Names (IDN) since last fall.
As part of the IDN system, domains with non-ASCII characters such as umlauts are translated from their natural Unicode form by your browser and other client software to a special encoding called punycode. This punycode is what is actually used in the DNS, registered with your domain registrar, etc.
Most Let’s Encrypt clients require you to enter the punycode form of the domain as opposed to the unicode form. Even if a client accepted the unicode form, the certificate it gets for you would contain the punycode form, because that’s what matters to the underlying technology.
If you do not know the punycode form of your domain, you can convert it using https://www.punycoder.com
If you are using the punycode form of your domain and you’re still having trouble issuing for a domain containing an umlaut, please open a topic in the Help section of the forum and answer all of the questions in the template.