A system for performing software updates for building devices of a building includes a thermostat associated with one of multiple zones of the building and a controller. The controller includes a processing circuit configured to store thermostat software in a memory device of the processing circuit, the stored software being software for the thermostat and determine, by communicating with the thermostat, whether thermostat software run on the thermostat is newer or older than the thermostat software stored in the memory device. The processing circuit is configured to update the thermostat software run on the thermostat with the thermostat software stored in the memory device in response to a determination that the thermostat software run on the thermostat is older than the thermostat software stored in the memory device and operate building equipment to control an environmental condition of the building.