Direct Digital Control (DDC) allows HVAC equipment to be controlled at an upper level (supervisory control) through commands from a central system, or at a lower-level (local-loop control) by local controllers. The various levels of equipment control can be allowed to interface through the building Energy Management and Control Systems. While implementing the Continuous Commissioning ® (CC ® ) 1 process in two institutional buildings, a number of operational and control issues related to the interfacing of equipment control have been identified. These issues include improper zone damper control of multi-zone air handling units (AHU) and comfort complaints related to room temperature control in a dual duct application, among others. These issues not only resulted in comfort problems, but also compromised building energy efficiency. All of the issues to some extent were related to the building HVAC equipment selection and design, and would have been costly to correct by redesigning and retrofitting the existing systems. This paper presents the CC measures identified in two case studies to improve building comfort and energy efficiency with minimal hardware investment.