This is a very short post because to be honest, I didn’t figure much out myself.
Add these to your application.env file:
3_ENABLED = "true" S3_BUCKET = "<bucket name>" S3_ENDPOINT = "https://<some-id>.r2.cloudflarestorage.com" S3_ALIAS_HOST = "<connected domain>" S3_PERMISSION = "private" AWS_ACCESS_KEY_ID = "<access_key>" AWS_SECRET_ACCESS_KEY = "<secret_access_key>"
The token/API key is a bit hard to find, but it’s on the top right.
Then (re)deploy your site.
I did set up a new server (my RPi4 started to struggle, and I guess if I'm half serious about Mastodon, I shouldn't host it at home), so I started afresh... But there's a way to migrate existing data to R2 as well, following this guide.