Abstract Background Extensive animal production systems, such as reindeer husbandry may represent a system to further study the context dependence of stress responses and the potential implications for animal welfare as research on food animal stress and welfare has so far primarily focused on animals in intensive animal production systems while animals from extensive production systems, such as reindeer, are yet underrepresented. We investigated short- and longer-term stress responses to repeated herding, handling and restraint and its potential effect on animal welfare in semi-domesticated adult female reindeer (Rangifer tarandus tarandus). We also assessed seasonal differences and the potential effect of the additional stressor of calf removal using serum concentrations of glucocorticoids (cortisol, cortisone and corticosterone), their precursors (11-desoxcortisol, 17-α-hydroxyprogesterone and deoxycorticosterone) and catecholamine metabolites (metanephrine and normetanephrine) in combination with the immunological stress proxy leukocyte coping capacity (LCC) and rectal temperature. Additionally, we assessed the interconnections among different stress indices and their suitability as stress indicators to evaluate handling-induced stress in reindeer, where rectal temperature, other than serum cortisol levels, emerged as a robust and integrative stress parameter. Results Herding, handling, and restraint elicited a marked and seasonally different short-term stress response with higher stress mediator levels in winter. Further, females who had their calf removed shortly after parturition showed increased stress levels based on LCC. The repeated exposure to the same stressors led to a habituation, with decreasing levels of stress indices to the procedure in both seasons. This outcome implies that reindeer females in the present study were able to cope well with repeated manipulations and that this intensification may not compromise animal welfare. Notably, the traditional stress index body temperature correlated with various stress indices encompassing the HPA axis response (cortisol and corticosterone in summer and additionally cortisone and 11-deoxycortisol in winter), the sympathetic-adrenal-medullary system (metanephrine) as well as the immunological response to stress (LCC), in both seasons. Conclusion Our results emphasise body (rectal) temperature as a robust and integrative stress parameter in the context of our study. Our findings add to a foundation for evaluating available stress indices in different individual and environmental contexts and may contribute to improved animal management practices aimed at reducing stress levels and enhancing animal welfare.