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Cloudflared can be configured to use Quad9 for DNS resolution via DNS over HTTPS (DoH).
In the cloudflared.yaml configuration file, replace the Cloudflare IPs in the proxy-dns-upstream section with the Quad9 addresses associated with your desired features:
proxy-dns-upstream: - https://22.214.171.124/dns-query - https://126.96.36.199/dns-query
proxy-dns-upstream: - https://188.8.131.52/dns-query - https://184.108.40.206/dns-query
proxy-dns-upstream: - https://[2620:fe::fe]/dns-query - https://[2620:fe::9]/dns-query