Conservation interventions increasingly involve active management of relative species abundances, especially when taxa of conservation concern are threatened by complex food web interactions. Unfortunately, the complexity of such interspecific interactions means that well-meaning management interventions can have unexpected, sometimes detrimental, effects on the species they are intended to protect. Here we report that the abrupt removal of an abundant non-native prey species (domestic sheep) and the cessation of predator control, actions intended to protect huemul deer Hippocamelus bisulcus in the future Patagonia National Park, appear to have had negative effects on this Endangered ungulate. During and following the changes in predator–prey management, predation of huemul fawns and females older than 1 year by native culpeo foxes Lycalopex culpaeus and pumas Puma concolor increased 3- and 5-fold, respectively. Predictions from demographic models suggest that elevated mortality rates of female huemul older than 1 year will, on average, cause this population of huemul to decline. These results highlight risks of unintended consequences when aggressive management actions are taken to protect taxa embedded in complex food webs. They also suggest that careful consideration of both inter- and intra-trophic level effects among all species in a system is warranted before conservation interventions are undertaken.