In this article, zooarchaeological evidence from 37 medieval and early modern sites in Estonia were assembled and examined. The analysis of over 69 000 mammal remains gave a comprehensive overview of the production and consumption of animal resources in the 13th to 18th century castles, towns, rural settlements, and one monastery. The focus was on domestic livestock: cattle, sheep, goats, pigs and horses. Cattle remains were most abundant, confirming it as the primary animal resource in the study period. Morphometrical analysis and tooth wear study supported the historical knowledge of a stronger tradition of draught oxen in the north and a possible focus on dairy husbandry in the south. Sheep and goat husbandry also had several purposes: kill-off times indicated lamb consumption and keeping the herd for wool and reproduction. Pigs, on the other hand, were raised only as a food resource. Stable carbon and nitrogen isotope analyses revealed differences in grazing areas and feed types between species and geographical regions. Compared to the main livestock, horses and also wild mammals had insignificant roles in providing primary resources but immense importance in manifesting status (horses and hunting) or in use for work and military purposes (horses). Overall, the animal husbandry of the Middle Ages and Early Modern Period developed towards the innovations and improvements of modern times, with native breeds being one example of the heritage of the past.