Understanding the conditions that force the implementation of management actions and their efficiency is crucial for conservation of endangered species. Wildlife managers are widely and increasingly using food supplementation for such species because the potentially immediate benefits may translate into rapid conservation improvements. Supplementary feeding can also pose risks eventually promoting undesired, unexpected, subtle, or indirect, and often unnoticed, effects that are generally poorly understood. For two decades, intensive food supplementation has been used in attempting to improve the breeding productivity of the Spanish Imperial Eagle, Aquila adalberti, one of the most endangered birds of prey in the world. Here, we examined the impact of this intensive management action on nestling health, including contamination, immunodepression, and acquisition of disease agents derived from supplementation techniques and provisioned food. Contrary to management expectations, we found that fed individuals were often inadvertently “medicated” with pharmaceuticals (antibiotics and antiparasitics) contained in supplementary food (domestic rabbits). Individuals fed with medicated rabbits showed a depressed immune system and a high prevalence and richness of pathogens compared with those with no or safe supplementary feeding using non-medicated wild rabbits. A higher presence of antibiotics (fluoroquinolones) was found in sick as opposed to healthy individuals among eaglets with supplementary feeding, which points directly toward a causal effect of these drugs in disease and other health impairments. This study represents a telling example of well-meaning management strategies not based on sound scientific evidence becoming a “contraindicated” action with detrimental repercussions undermining possible beneficial effects by increasing the impact of stochastic factors on extinction risk of endangered wildlife.