Hunting activity is usually seen as a factor capable of causing an intense stress response in wildlife that may lead to short but also long-term stress. In the Lousã Mountain, Portugal, the population of red deer (Cervus elaphus) is the target of intensive seasonal hunting. We collected and measured cortisol (and its metabolites) in three tissues types (blood, feces and hair) from red deer hunted during two hunting seasons to evaluate the stress levels at different time windows. We also assessed the immunological and physical condition of the animals. We predicted that the hunting activity would act as a stressor inducing increased short and long-term stress levels in the population. Results showed an increase in hair cortisol levels during the months of harvesting. Surprisingly, the tendency for plasma cortisol levels was to decrease during the hunting season, which could be interpreted as habituation to hunting activity, or due to the hunting duration. Contrary to our predictions, fecal cortisol metabolites did not show any clear patterns across the months. Overall, our results suggest an influence of hunting activities on the physiological stress in red deer. In addition, hair seems to be useful to measure physiological stress, although more studies are required to fully understand its suitability as an indicator of long-term stress. Methodologically, our approach highlights the importance of simultaneously using different methods to assess short and long-term effects in studies on physiological stress reactions.