GeneSat will be controlled using a distributed mission control system developed by students, staff and faculty from Santa Clara University's Robotic Systems Laboratory. This group will also serve as the mission control team for realtime contact operations with the satellite.

Command and control of the vehicle will be performed from a number of control nodes. The primary and backup nodes are located in the NASA Ames Research Center's Multi-Mission Operations Center and at the CREST Mission Control Center, respectively. These control nodes communicate via the internet with the SRI 60-ft communication station, located in the Palo Alto foothills. This station tracks the satellite when visible in order to transmit commands and to receive telemetry. Signals from GeneSat's amateur radio beacon will be received by additional communication stations operated by CREST universities as well as by HAM radio operators throughout the world.