<p>Hair cortisol can be used as a biomarker of chronic stress which makes it a valuable indicator of animal welfare. This study aimed to evaluate hair cortisol as a measure of welfare in dairy cows kept in mixed systems (confinement + grazing) in compost barn (CB) or outdoor soil-bedded (OD) during two different calving seasons. Dairy cows had access to grazing for half a day and then were supplemented in a confined area according to treatment. CB: with sprinkling and ventilation; OD: with dirt floor and a shaded area. The experiment was carried out with cows calving in autumn (<i>n</i> = 28) and winter (<i>n</i> = 26). Hair samples were obtained 21 days before (-21 DRC), at 90 and 180 days after calving (DRC 0 = calving). Fixed effects were treatment, time relative to calving and the interaction between them. No differences were found between treatments and treatment x time interaction in either calving season. In autumn calving cows, hair cortisol of both treatments increased at 90 DRC relative to prepartum (<i>P</i> = 0.01), dropping at 180 DRC (<i>P</i> = 0.02). In winter calving cows, during prepartum hair cortisol in both treatments was lower than at 90 DRC and 180 DRC (<i>P</i> = 0.004). In this study, hair cortisol did not differ between dairy cows kept in mixed systems in CB or OD in both calving seasons. However, cortisol levels were different throughout lactation in the two calving seasons, remaining at high levels at 180 days in cows that calved in winter, indicating heat stress.</p>