Various embodiments include network computing devices and methods for managing Domain Name Service (DNS) over Hypertext Transfer Protocol Secure (DoH). A processor of a network computing device may receive from a client computing device a DoH request comprising a public certificate associated with a client identifier. The processor may generate a fingerprint of the public certificate. The processor may obtain a client-specific DoH policy based on an association between the fingerprint of the public certificate and the client-specific DoH policy. The processor may apply the DoH policy to the DoH request to formulate a response to the DoH request.