A system and method for retention of flight deck preferences operates to control a comprehensive combination of aircraft systems and system configurations enabling a pilot to seamlessly retain and recall the desired preferences based on a plurality of mission related factors. With system control of flight deck physical settings including seat position and shape, display illumination and color and internal and external lighting configurations, the system allows a pilot to save time, effort, and minimize errors of system set up and configuration. With a short entry, or short-range sensing, of the pilot ID, the pilot commands the system and method for retention of flight deck preferences to configure each of the plurality of aircraft systems according to the recalled pilot preference.