Disclosed are various embodiments for a remotely-hosted auto-discovery service. An auto-discovery request received from a client device over a network can be accessed to identify a domain associated with the auto-discovery request. A digital certificate corresponding to the domain can be identified and a configuration file can be generated for a web server application that creates at least one virtual host for a uniform resource locator (URL) identified in the auto-discovery request. The digital certificate can be bound to the at least one virtual host to operate a secure connection with the client device. An enrollment response can be generated for communication to the client device over the network.