An HVAC controller may have an operational mode in which the HVAC controller provides operational instructions, and a commissioning mode in which a plurality of wireless devices can be enrolled. While in the commissioning mode, the HVAC controller is configured to accept a first input from a user via the user interface that designates a first zone of the plurality of zones and causes each of two or more first wireless devices that are subsequently placed in an enrollment mode by the user to be enrolled in the first zone, and to subsequently accept a second input from the user via the user interface that designates a second zone of the plurality of zones and causes each of two or more second wireless devices that are subsequently placed in an enrollment mode by the user to be enrolled in the second zone.