The beginning of husbandry in the Iberian Peninsula has been documented from the second half of the 6th millennium BCE and was based on the breeding of domestic caprines, mainly sheep. The first evidence of these practices comes from the Mediterranean region, but they quickly expanded inland. Previous studies have reported on the importance of the El Mirador sheepfold cave (Sierra de Atapuerca, Burgos, Spain) for understanding the process of the adoption of a farming economy in this inland region. In this study, we focus on husbandry and sheep management occurring in the 6th and 5th millennium cal BCE occupations of El Mirador cave by means of sequential oxygen (δ18O) and carbon (δ13C) isotope analyses in sheep molar tooth enamel. The results show a rapid adaptation and adoption of domestic sheep in the inland of the Iberian Peninsula. In El Mirador cave, well-organised sheep breeding was developed based on the concentration of births at the end of winter and early spring, for a period of ~2.64 months, which made husbandry more compatible with other economic activities. In 5th millennium levels, autumn births were also documented and may be indicative of the intervention of the shepherd in the reproductive cycle of the sheep and of a progressive adaptation of these animals to the interior of the Peninsula. All these strategies may have been supported by the recurrent occupations of the sheepfold, flocks grazing in the areas surrounding the cave and the possible use of leaf fodder in winter.