Mission establishments in Alta California and elsewhere were home to complex, pluralistic communities in which native peoples actively but differentially negotiated aspects of colonialism through daily practice and the reinterpretation of identity. To explore these issues, we compare the archaeological evidence from two different indigenous dwellings at California’s Mission Santa Clara de Asís: an adobe barracks and a native-style thatched house. In particular, we consider possible differences between the dwellings’ inhabitants in terms of relative status, ethnolinguistic affiliation, and re-articulation of indigenous traditions.