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You said Traefik is getting certs from Cloudflare, but do you mean it's getting Let's Encrypt certs using a CF DNS challenge? And if that is the case, then your browser should trust the Traefik endpoint since LE certs are publicly trusted.
Are you sure you're hitting Traefik when you get a cert warning? You need to update your internal DNS if not.
You're right, I'm using the cloudflare DNS challenge to get let's encrypt certs. I'm definitely hitting traefik. I'm testing by turning the Wi-Fi on my phone off/on and opening the page after. I get the same cert every time but it's not trusted when on Wi-Fi. This makes sense since it's the origin server cert which is meant to encrypt traffic between my server and cloudflare. To add more certainty, when Wi-Fi is on, a traceroute shows only one hop to my server and shows a bunch of hops when it's off.
If you, Traefik, and your origin server are on the same network, then it's going to be one hop regardless of whether you're hitting the Traefik proxy or the origin server. If Traefik is serving up the origin server's cert and not the LE cert, then Traefik is misconfigured to pass through instead of proxy, but I'm still not sure that's the case as it's almost harder to configure it that way than the correct way as a proxy.
What IP:port is your origin server listening on, what IP:port is Traefik listening on, and how is Traefik configured to reach the origin server?
When I turn off Wi-Fi, I'm not on the same network as my server, it's my carrier network so all the internet hops are expected.
The way it's working now is I have a domain (example.com) that is set up on cloudflare DNS. I added a tunnel in cloudflare zero trust, which generates certificates you add to your server to encrypt traffic from your server to cloudflare. I have added these to traefik to be served with my service url (service.example.com). Then, I added a route in cloudflare for service.example.com.
This works fine. But, what I've also done is add a local DNS entry for service.example.com so when I'm on my LAN, I access it without going out to the internet and back (seems like a waste). However, this is serving the origin server certs from cloudflare, which causes trust issues
I'm using docker for everything: traefik, cloudflared tunnel, and my services on the same hardware. The tunnel just runs, and it's configured on cloudflare zero trust to talk directly to the container:port over the docker network.
In that case, if CF is taking to Traefik and not the actual origin server, you just need to forget about the origin certs altogether and use LE certs in Traefik.