Human activities are altering ecosystems and threatening the well-being of wildlife. The study of the stressful effects of human disturbances on animal distribution, physiology and behaviour can provide fundamental insights for wildlife conservation. Here, we assess how two declining birds, the European Roller Coracias garrulus and the European Scops Owl Otus scops, cope with alteration by human activities in farming habitats of the south of Spain. We studied nest distribution, quantified nestling physiology (corticosterone levels in plasma and feathers and body weight close to fledgling) and parental behaviour (feeding rates) of both species along a human alteration gradient. Rollers and Scops Owls used the same type of habitat and their spatial distribution was not determined by individual quality. In Rollers, nestlings raised in scrubland areas had high stress-induced corticosterone levels, possibly due to high predation risk in this habitat. In addition, Rollers and Scops Owls showed opposite relationships with farming activity and human disturbance. Nestling Rollers showed the highest corticosterone levels in feathers, weight and parental feeding rates in areas with intense farming activity. These results suggest that despite the disturbance produced by farming activities, inducing a higher stress in these areas, cultivated areas may, simultaneously, provide parents with a higher abundance of prey which would trigger increased feeding rates and, hence, higher nestling weights. Furthermore, nestling Scops Owls showed the highest stress-induced corticosterone levels in areas close to roads, suggesting that they would be affected by human disturbance due to infrastructures that disturb also at night when Scops Owls are active. Therefore, susceptibility to human disturbance may vary between species, probably due to variation in the daily pattern of human activities and the species’ activity rhythm, buffering or exacerbating the effects, which should be considered in future studies on human alterations and birds.