I don't think Pi-Hole can query DoT and DoH resolvers directly. People usually set up unbound or AdGuard's dnsproxy, configure it to forward queries to the DoT/DoH resolver and set it as Pi-Hole's upstream resolver.
this post was submitted on 31 Oct 2025
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This.
As someone that has their Pihole talking to DoH Mullvad upstream, what is described above is exactly how I did it.
You could use Blocky for this. It can do both, apply some block lists and use DoT/DoH resolvers.
I switched from pihole to Blocky and I love it way more. Works like a charm with dnscrpyt and android