Certificates not issued despite domain being verified

Hey team!

Context: I’m using Cloudflare for my DNS. Have seen many other posts that is facing the same issue, but I could not seem to solve mine.

I have added A, AAAA and CNAME (_acme-challenge), all without Cloudflare proxies, to the domain nodeflair.com and it seemed like it helped in validating the domain but doesn’t issue the certificate. I do have other A records pointing to other servers as the app is in production so I could not remove them as it will cause downtime.

The certificate issuing for www.nodeflair.com works very well on the other hand (as there’s not other A records)

I’ve tried removing and re-adding the certificate, but still not getting anything.

Any ideas?


I sometimes get them instantly, and other times it takes a few hours.

LetsEncyrpt has rate limiting that I believe impacts this. It may not be related to Cloudflare or Fly at all.

Of the 5 certs I did in the last week, 1 was instant, 2 were 20-30 minutes, 1 was a hour, and another was 4 hours.

I manage to get it working but just want to share my experience with everyone.


  • Disable Universal SSL according to Custom Domains and SSL Certificates · Fly Docsunfortunately it caused downtime for my app instantly

  • During the downtime, I removed all the non relevant A records and attempt to validate, but it does not work too.

  • Removed the existing TXT records _acme-challenge and dig txt _acme-challenge.mydomain.com+short returns the result from flydns.net. However,it does not issue the certificate either.

  • Tried re-issuing it and it doesn’t work (instantly) - However, ~15 mins after it, it got issued. Not sure if it’s a coincidence or causation.

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