This dataset contains data collected during the analyses of archaeological mammal remains from 37 medieval and early modern sites in Estonia. The dataset consists of four tables: 1) information on archaeological sites, 2) identifications, 3) cattle metacarpal morphometrics, 4) stable isotope data. It is being made public both to act as supplementary data for the research project PRG29 and for the publication Rannamäe, E. & Aguraiuja-Lätti, Ü. 2023. Zooarchaeology of livestock and game in medieval and early modern Estonia. Estonian Journal of Archaeology, 27, 3S, 50–82, https://doi.org/10.3176/arch.2023.3S.03.