Archaeological investigations at Mission San José in Fremont, California, have revealed large areas of the mission landscape, including portions of two adobe dwellings in the mission’s Native American neighborhood. Preliminary synthesis of previous and ongoing research at Mission San José focuses on the implications of archaeological evidence for understanding the persistence of indigenous cultural practices under missionization. Materials considered include flaked stone artifacts, shell and glass beads, modified ceramic disks, and faunal and floral remains. Our findings suggest that native people rearticulated various practices within the mission, but did so in ways that were consistent with existing traditions and cultural knowledge.