In the archaeological tradition of what is today Peru, studies of sedentary agricultural groups have accorded a minor role to the analysis of stone tools relative to other suites of material culture. Here, we illustrate the value of such lithic collections via a case study of settlement sites from the Chachapoyas region of northern Peru (AD 300–1500). This study demonstrates the potential of methods such as use-wear microscopy and raw material analysis to address questions of theoretical interest to archaeologists studying sedentary society, such as subsistence, household behavior, and ceremonial practices. A set of generalized linear models of the spatial distribution of volcanic stone indicates that lithic raw material acquisition at these ceramic period sites was likely embedded in other activities. In addition, we examine an unusual set of limestone and carbonate-patinated artifacts that suggest that lithic procurement and selection were informed and strategic, if not conforming to expected technological priorities. We suggest that, by taking the potential value of lithic artifacts into consideration from project design through field collection and assemblage sampling, researchers can minimize biases that may otherwise limit the value of lithic assemblages.