In continuously changing environments, variation of different ecological factors could affect the functioning of the hypothalamic-pituitary-adrenal (HPA) axis in wild mammals, increasing the secretion of glucocorticoids (GCs). In different animal species, GC concentrations are often used as a measure of the physiological stress response to environmental pressures, such as fluctuations in food abundance, population density, intra- and interspecific competition, and predation risk. However, previous studies reported contrasting results or did not find clear associations between physiological stress and environmental variables. Here, we used concentrations of faecal glucocorticoid metabolites (FGMs) as an integrated measure of physiological stress in wild Eurasian red squirrels (Sciurus vulgaris) from three study areas in the Italian Alps, to investigate whether variations in conifer-seed crop size and/or population density affected HPA axis activity. Squirrel density was estimated in each trapping session using the minimum number of animals alive, and annual counts of fresh cones from different conifer species were used to estimate annual food abundance (MJ/ha). We expected higher FGMs in response to increasing population density and/or decreasing food abundance, since these two variables could act as environmental stressors. Our results showed a lack of association between population density and FGMs and a significant effect of food abundance on FGMs. When conifer seed-crops were poor to moderate, FGMs increased with food abundance, while in the range of high seed-crops, FGMs remained first constant and then slightly decreased with a further increase in seed abundance. We also found differences in FGMs among seasons, as previously observed in this species. Our study adds further evidence that physiological stress can be influenced in different ways by environmental pressures and that long-term studies using individually marked animals are needed to disentangle the potential adaptive outcome of the physiological stress response in pulsed resource systems.