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Yes, definitely!

Pihole is basically just a "pimped" dns server.

So, to rephrase your question: "is it possible to run both a VPN server and continue running a dns server?"

It works like a charm indeed, I run the WireGuard client on all my devices (laptop, phone, tablet) in on-demand activation mode (VPN activates whenever I leave my home WiFi), and configured them them to use the PiHole server as DNS, so I have ad-blocking on all my devices, all the time. I don't perceive any kind of negative effect on network performance (it helps to have fiber with symmetric up/down speeds for this setup)

Is it possible to set it up like this: I want to use mullvad VPN, so my IP/location is obfuscated, but still to have PiHole? So something like I connect my laptop and mobile to my router -> RPi -> mullvad VPN -> internet. If it is, how can I achieve it?

With Wireguard you set DNS server IP directly in the config file, it is not negotiable over the connection. So you can edit the config to set it to your pihole's ip. Or remove the DNS line altogether and then it won't touch your DNS settings at all.

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