A method for selecting a communication protocol for a virtual desktop instance in a service provider environment may include providing to a client computing device, access to a virtual desktop instance running on a server computer using a first communication channel associated with a first communication protocol. A request for functionality from a user of the device is detected, the requested functionality being unsupported by the first communication protocol. A second communication protocol from a plurality of available communication protocols may be selecting based on the requested functionality. The second communication protocol may support the requested functionality. A user authorization for using the second communication protocol can be verified. Upon successful verification, a second communication channel is established between the server computer and the device using the second communication protocol for performing the functionality, while maintaining access to the virtual desktop instance using the first communication channel.