The building foundations of the Todos los Santos Church are the only tangible heritage associated with Spanish colonial history in Taiwan. The church and its associated cemetery are located on the small island of Heping Dao, off Keelung, on the northern coast of Taiwan. This major colonial settlement was successively occupied by the Spanish, Dutch and Chinese during the 17th and 18th centuries, in conjunction with Taiwanese Aboriginals and other Asian communities. Twenty burials were revealed by archaeological excavations carried out between 2011 and 2019 by an international team of researchers, led by a Spanish and Taiwanese scientific consortium. They are located at the west end, both inside and outside of the church. They follow two distinct and perpendicular orientations and display various body treatments. In this paper, we use data generated by archaeology, archaeothanatology, and archaeogenetic studies to analyse this distinctive spatial patterning. Our results show that the distribution of the burials is strongly dependent on individual biological identity, defined by age-at-death, sex and ancestry of the dead, reflecting on the different occupation periods, social structures, and life history of the Keelung colony during a period of strengthened interactions.