Leadership in Energy and Environmental Design and building commissioning are two eco-innovations that have contributed to the long-term efficiency and sustainability of new-building construction. The Leadership in Energy and Environmental Design system promotes green, efficient, and sustainable design and construction. Building commissioning is a quality process used to verify that the owner’s project requirements are being met by the final design, construction, and operations and maintenance. Quality function deployment has been successfully used in product development to capture the voice of the customer, translating it into engineering characteristics and then carrying the parameters into production and service to ensure the voice of the customer is met with the final product. To provide the next level of eco-innovation for commissioning and Leadership in Energy and Environmental Design, the four-phase quality function deployment model will be adapted to, and integrated with, the commissioning and Leadership in Energy and Environmental Design processes. The adapted model can effectively link the project phases to ensure the owner’s project requirements for Leadership in Energy and Environmental Design are met with the final building. The primary objective of this research is to develop an integrative and systematic methodology to adapt the four-phase quality function deployment model to the commissioning process of new-building construction, to provide practitioners the steps to take the adapted model through the commissioning process as a means to oversee the entire design and construction quality process, ensuring the owner’s Leadership in Energy and Environmental Design goals are integrated into the design and carried through construction to the operations and maintenance phase for long-term efficiency and sustainability.