I have Wireguard installed on a Raspberry Pi using pivpn, and Pihole running in a docker container on the same Pi. I have been setting Pihole as the dns individually, for each device.

My phone connects fine using pivpn -qr and pihole works perfectly. For my Linux Mint laptop, I followed the instructions on the pivpn website and I can access services through IP address, but not through the dns records in Pihole, both with Wireguard disabled, and with it enabled and the laptop on a different network. Weirdly, Pihole does work with Wireguard enabled and the laptop connected to the same network.

I have checked the dns settings in the wireguard server, the wireguard client config, and the laptop wifi settings. I have also tried removing and reinstalling the wireguard client and restarting the laptop.