Can I use pregenerated pem files?

We have a server, where as much as possible should be handled by the installed plesk instance.

Plesk can create pem files for certificates.

Is it possible to use these with the letsencrypt client?

What’s in the PEM files? Are they certificate signing requests (CSRs) plus associated private keys? Or something else?

Yes, CSR with associated provate key. I should have mentioned it in the original question.

You can use [this client][1] to sign your certificate.

Usage:

python sign_csr.py --public-key user.pub domain.csr > signed.crt

(note: run it in screen or tmux as it will ask you to sign some files)
[1]: https://github.com/diafygi/letsencrypt-nosudo