I've been noticing a similar issue with my HomeKit-enabled eero Pro - I have not defined ANY fallback DNS server so all DNS requests _should_ be going to the PiHole. Despite this, I can't seem to see very much. Also ensured that Local DNS Caching has been disabled (via Settings > Advabced > eero Labs)

I found this thread because I'm having the same issue. Also trying to have Eero configured to use my PiHole as the primary dns. 

Same issue here...following

Also having this issue and have disabled HomeKit on my eero for now. 

I have been having the exact same issue and, yes, disabling HomeKit fixes it but...I don't want to disable HomeKit. Is this officially a bug Eero is looking into?

This must be a bug, but it is has more severe issues. I lose full DNS functionality at random times, making it appear as if everything is offline. I’m concerned about disabling HomeKit if that means I have set up ~50 Homekit devices again. Will they really be removed from HomeKit? Can I remove eero via the Home app without affecting other HomeKit devices?

Many thanks russw , my pi-hole wasn't working at all after I set up my new Eero and I was pulling my hair out trying to figure out why. Disabling HomeKit immediately fixed it for me. 

Eero really need to look into this as enabling HomeKit clearly breaks custom DNS.

I did eventually disable HomKit in eero and it resolved the headache from apparent drop-offs. It could be a combination with safety filters causing it, which also "hijacks" DNS to protect against content you want filtered out. I now see a huge speed improvement in loading content after setting up 1.1.1.2 and 1.0.0.2 as a custom DNS and disabling HomeKit and safety filters. I still have safety filters enabled for the kids in the house which may impact their perceived performance. 1.1.1.2 is CloudFlare's new DNS which also "protects" against sites you want to avoid. (I am running pi-hole for ad filtering, with 1.1.1.2 as the upstream DNS, on one laptop as an experiment--it has been working well so far.)

same issue here, Eero could implement a serious DNS server to solve this issue...DNS cache don't solve it! I think it's necessary activate also IGMP snooping

This is still an issue.  Running 6.3.0

Turned on Homekit integration as soon as I noticed that my Pro 6 got the update and BAM! Network down across the board until I stopped using my local Pi-hole server pair as the custom DNS addresses on the eero. I was running pi-hole locally passing thru DNScrypt out to NextDNS - thankfully I was able to use the NextDNS servers instead but they're only good until my external IP changes and then I gotta relink it. Or set up DDNS but man. Homekit integration broke my local pi-hole setup real bad. Not super happy about it.

can confirm the issue is still there. We do need a fix because since it's possible to configure the DNS I would expect requests to be forwarded, but it's not happening at all.

Issue still persists with the latest 6.5.0 firmware. Could anyone from the eero team please tell us if this is due to a limitation of the Homekit integration and it cannot be fixed, or if they are working on a fix? I am willing to disable the Homekit integration if this cannot be fixed.

Thanks