During the New Kingdom, Egypt began a military campaign to regain command over Nubia. Extremely successful, their control extended to the fourth cataract by the time of Thutmose III. The circumstances of this power, however, are not well known. It is unclear whether Egyptian colonists or locals administered Nubia during this time. Using a bioarchaeological approach via the study of human skeletal remains and archaeological data from the New Kingdom site of Tombos in Nubia and comparative Egyptian and Nubian skeletal samples, this paper addresses these long-standing questions. Analyses suggest that the Tombos individuals were an ethnically and biologically mixed group. The examination of health indicators suggests that the people of Tombos endured a relatively high degree of physiological stress, despite possible resources obtained through trade networks. Additionally, the Egyptianisation of Nubians at Tombos may have provided a peaceful environment in which few traumatic injuries were seen.