This paper examines the archaeology of mortuary contexts in Colonial Peru (16th-17th centuries). In doing so, I demonstrate both the importance of mortuary analysis in studies of colonial contexts in this region as well as to see what can be learned about the active and fluctuating nature of religious and social interactions between early Spanish Catholic colonists and Indigenous Andean communities. My thesis comparatively analyzes three case studies of sites of intense early colonial conversion efforts, giving appropriate historic context to the variability in both Spanish and Indigenous agendas and the social and religious history of each region. I summarize existing, and apply new, mortuary studies to the research of each of these three case studies; the Collagua of the Colca Valley, the Muchik of the Lambayeque Valley, and the resettled groups at Magdalena de Cao in the Chicama Valley. In each of these three case studies, viewing the early interactions between Spanish and Indigenous groups through the lens of changing mortuary traditions and interactions with the dead yielded insights into the active negotiation of hybrid practices in these regions, which I argue is support for the need of further research in this field.