In this article, we present an isotopic perspective of key research questions in Andean bioarchaeology, focusing on the ways in which stable and radiogenic isotope analyses have contributed to our understanding of the past. Andean archaeology offers a window into long-term processes of economic, socioecological and political change since the mid-Holocene, thus providing historical trajectories of socio-ecological change relevant for global comparison. The spatial scale of this review includes the areas traditionally identified as the south-central Andes and the southern Andes. These ecological scenarios are characterised by marked topographic, climatic and ecological variations that are fruitful for the application of isotopes to understand diet, mobility, migration and ritual in past human societies. Within the broader Andean context, here we focus on the growth of bioarchaeological applications of isotopic data. We discuss some major themes of economic production, mobility and exploitation of environmental diversity, maize agriculture, migrations in small- and large-scale societies and ritual practices related to human sacrifices and body modifications. Building on this, we discuss theoretical and methodological trends and directions for future research combining bioarchaeology and isotopes in the Andes.