Glucocorticoids such as cortisol are released during stressful events. However, many of the effects of cortisol on animals in the wild are still poorly documented. We evaluated the effects of artificially elevated cortisol on diet and morphology over the short term (2 weeks) and long term (4 months) using a wild population of juvenile semi-anadromous brown trout (Salmo trutta) in Denmark. We caught, tagged and manipulated juvenile fish while in their natal freshwater streams in the fall. Manipulations consisted of an exogenous intracoelomic injection of cortisol suspended in vegetable shortening (designed to mimic an extreme physiological challenge), a sham group (injection of vegetable shortening) and a control group (tagged only). We then recaptured fish 2 weeks later and again after 4 months. We assessed diet using stable isotopes from plasma (short term) and scales (long term), and morphology using geometric morphometrics. Cortisol affected carbon stable isotope signatures but had minimal effects on nitrogen isotopes and morphology. Irrespective of treatment, carbon and nitrogen stable isotope values increased over time. This study shows that cortisol can have both short and long term effects on individuals in the wild.