Depending on the habitats they live in, temperate ungulates have adapted to different degrees to seasonally changing forage and weather conditions, and to specific escape strategies from predators. Alpine chamois, a mountain ungulate, and red deer, originally adapted to open plains, would therefore be expected to differ in their physiological responses to potential stressors. Based on 742 chamois and 1557 red deer fecal samples collected year‐round every 2 weeks for 4 years at the same locations within a strictly protected area in the Swiss Alps, we analyzed glucocorticoid metabolite (FGM) concentrations for both species. Results from linear mixed effects models revealed no physiological stress response to changing visitor numbers, but instead to drought conditions for both species during summer. In winter, FGM concentrations increased with increasing snow height in both species, but this response was modulated by temperature in red deer. Chamois showed a stronger stress response to increasing snow height during November and December than between January and March, while FGM concentrations increased with decreasing temperature throughout winter. An increase in FGM concentrations with decreasing forage digestibility during winter was found only for red deer. The results are thus partly in contradiction to expectations based on feeding type and adaptations to different habitats between the two species. The lack of a response to forage digestibility in chamois may reflect either better adaptation to difficult feeding conditions in subalpine forests, or, by contrast, strong constraints imposed by forage quality. The similar responses of both species to weather conditions in winter suggest that climatic factors at the elevations examined here are sufficiently harsh to be limiting to temperate ungulates regardless of their specific adaptations to this environment.