Systems and methods for generating multiple registrations is provided. An image depicting a portion of a patient's anatomy and a tracking device affixed to an accurate robot may be received. A first registration of a patient coordinate space to a robotic coordinate space may be generated based on the image. A second registration of the patient coordinate space to a navigation coordinate space based at least in part on a position of second markers on the tracking device detected by a navigation system may be generated. The first registration and the second registration may be independent of each other.