A three-dimensional adjustable door mounting system and method for aligning and installing a hinged door within a frame. In one embodiment, the mounting system includes one or more captive nuts mounted to the door. The captive nut includes a movable adjusting plate retained by a stationary holding bracket mounted to the door. A threaded fastener inserted through a hinge door leaf and into the adjusting plate allows an installer to move and adjust the position of the hinge relative to the door in a first plane. In other embodiments, captive nuts may further be affixed to the door frame. A threaded fastener inserted through a hinge frame leaf and into the adjusting plate allows an installer to move and adjust the position of the hinge and door relative to the frame in a second plane different than the first plane.