Having configured DNS-Over-HTTPS, I expect to run dig @127.0.0.1 -p 5053 google.com and receive a reply
dig @127.0.0.1 -p 5053 google.com
; <<>> DiG 9.11.5-P4-5.1+deb10u1-Raspbian <<>> @127.0.0.1 -p 5053 google.com
; (1 server found)
;; global options: +cmd
;; connection timed out; no servers could be reached
Pi-hole does not support sending or receiving DoH queries.
You should consider consulting your DoH software provider, whatever your choice of DoH software is.
Hmmm, OK...I was however using the official instructions here - Redirecting...
Are you therefore saying this is a Cloudflared issue, not a Pi-hole issue?
Either that, or you've missed a step in setting up cloudflared.
Since you are directing your dig query to a certain localhost port, check what's listening on that port on your Pi-hole machine :
sudo ss -tulpn 'sport = :5053'
It seems nothing?
sudo ss -tulpn 'sport = :5053'
Netid State Recv-Q Send-Q Local Address:Port Peer Address:Port
Then cloudflared wasn't started or failed to start.
What did the status check from the instructions reveal?
sudo systemctl status cloudflared
● cloudflared.service - cloudflared DNS over HTPPS proxy
Loaded: loaded (/etc/systemd/system/cloudflared.service; enabled; vendor preset: enabled)
Active: inactive (dead) since Thu 2020-07-30 13:02:12 BST; 3s ago
Process: 26440 ExecStart=/usr/local/bin/cloudflared proxy-dns $CLOUDFLARED_OPTS (code=exited, status=0/SUCCESS)
Main PID: 26440 (code=exited, status=0/SUCCESS)
Jul 30 13:02:12 raspberrypi cloudflared[26440]: cloudflared proxy-dns [command options]
Jul 30 13:02:12 raspberrypi cloudflared[26440]: OPTIONS:
Jul 30 13:02:12 raspberrypi cloudflared[26440]: --metrics value Listen address for metrics reporting. (default: "l
Jul 30 13:02:12 raspberrypi cloudflared[26440]: --address value Listen address for the DNS over HTTPS proxy server
Jul 30 13:02:12 raspberrypi cloudflared[26440]: --port value Listen on given port for the DNS over HTTPS proxy
Jul 30 13:02:12 raspberrypi cloudflared[26440]: --upstream value Upstream endpoint URL, you can specify multiple en
Jul 30 13:02:12 raspberrypi cloudflared[26440]: --bootstrap value bootstrap endpoint URL, you can specify multiple e
Jul 30 13:02:12 raspberrypi cloudflared[26440]: --help, -h show help (default: false)
Jul 30 13:02:12 raspberrypi cloudflared[26440]:
Jul 30 13:02:12 raspberrypi systemd[1]: cloudflared.service: Succeeded.
Showing cloudflared as inactive, as expected somehow.
Running systemctl status with full output may have additional hints why it does so:
sudo systemctl status cloudflared --full --no-pager
You did provide command line options, didn't you?
You'd have to sort why cloudflared would fail after starting on your system.
Here's the output of the systemctl status query:
sudo systemctl status cloudflared --full --no-pager
● cloudflared.service - cloudflared DNS over HTPPS proxy
Loaded: loaded (/etc/systemd/system/cloudflared.service; enabled; vendor preset: enabled)
Active: inactive (dead) since Thu 2020-07-30 13:17:45 BST; 5min ago
Process: 3069 ExecStart=/usr/local/bin/cloudflared proxy-dns $CLOUDFLARED_OPTS (code=exited, status=0/SUCCESS)
Main PID: 3069 (code=exited, status=0/SUCCESS)
Jul 30 13:17:45 raspberrypi cloudflared[3069]: cloudflared proxy-dns [command options]
Jul 30 13:17:45 raspberrypi cloudflared[3069]: OPTIONS:
Jul 30 13:17:45 raspberrypi cloudflared[3069]: --metrics value Listen address for metrics reporting. (default: "localhost:") [$TUNNEL_METRICS]
Jul 30 13:17:45 raspberrypi cloudflared[3069]: --address value Listen address for the DNS over HTTPS proxy server. (default: "localhost") [$TUNNEL_DNS_ADDRESS]
Jul 30 13:17:45 raspberrypi cloudflared[3069]: --port value Listen on given port for the DNS over HTTPS proxy server. (default: 53) [$TUNNEL_DNS_PORT]
Jul 30 13:17:45 raspberrypi cloudflared[3069]: --upstream value Upstream endpoint URL, you can specify multiple endpoints for redundancy. (default: "https://1.1.1.1/dns-query") [$TUNNEL_DNS_UPSTREAM]
Jul 30 13:17:45 raspberrypi cloudflared[3069]: --bootstrap value bootstrap endpoint URL, you can specify multiple endpoints for redundancy. (default: "https://162.159.36.1/dns-query", "https://162.159.46.1/dns-query", "https://[2606:4700:4700::1111]/dns-query", "https://[2606:4700:4700::1001]/dns-query") [$TUNNEL_DNS_BOOTSTRAP]
Jul 30 13:17:45 raspberrypi cloudflared[3069]: --help, -h show help (default: false)
Jul 30 13:17:45 raspberrypi cloudflared[3069]:
Jul 30 13:17:45 raspberrypi systemd[1]: cloudflared.service: Succeeded.
It doesn't provide me with any hints, but might to others?
Yes, I provided command line options, as per the manual method of setting up
(You can format your output for readability by using the </> Preformatted text menu option. I’ve just done that for you 
)
It doesn't quite seem cloudflared would know about those options and tries to go by its defaults (but then, I am not using cloudflared at all).
What's the output of
ls -lah /etc/default/cloudflared
cat /etc/default/cloudflared
cat /etc/systemd/system/cloudflared.service
I've now resolved this with a fresh install of OS/Pi-hole and an auto install of cloudflared
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