Use dnscrypt-proxy https://github.com/jedisct1/dnscrypt-proxy

You could also run your own DNS server as well, like Core DNS, and configure it to resolve through DNS-over-HTTPS. I'm sure this is about the same thing, but it's worth noting that you could possibly use your existing router or NAS to run the software.

Thanks a ton, this looks fantastic! Do you know if it's possible to setup Pihole to use this (and possibly other features) but not do any adblocking?

I'm using cloudflared [0] for this. Allows me to have system level DoH and everything uses it (unless explicitly configured not to). Working on Linux machines (amd64 and aarch64) and MacOS.

The documentation is not great / accurate but with a bit of fiddling I have it running as a systemd service (launchctl on MacOS). I'm using the /metrics endpoint to get details in Prometheus on the stats.

0. https://github.com/cloudflare/cloudflared

Sure, just deselect the blocklists in the GUI of your pi-hole.