International conservation efforts and prohibitionary drug intersect in unexpected ways throughout the Mesoamerican Biological Corridor (MBC). US-led counterdrug interdiction of transnational cocaine trafficking, or ‘narco-trafficking’, is increasingly pushing narco-traffickers and their associated environmental destruction into protected areas (PAs) to establish new smuggling routes. These locations are also where the greatest densities of jaguars (Panthera onca), an iconic and declining species, are found in Central America. Intersecting two geospatial datasets estimating 1) jaguar densities and 2) changes in landscape suitability for drug trafficking following counterdrug interdiction pressure, we estimated that roughly 69 % of the estimated population of jaguars in the MBC were found in areas of increased suitability for narco-traffickers. Moreover, jaguar populations within PAs were 2.5 and 34 times more likely to be in increased narco-trafficking suitability areas than those in jaguar corridors or other area without conservation designations, respectively. These findings illustrate the full costs of continuing current counterdrug interdiction policies alongside conventional conservation strategies and suggest that community-based conservation governance may more effectively discourage narco-trafficking activities and enhance conservation outcomes. •Supply-side counterdrug interdiction pushes cocaine trafficking, or ‘narco-trafficking’, activities into remote areas•Jaguars in protected areas and corridors are at greater risk from clandestine activities than those in non-protected areas•Full accounting of collateral damages from U.S. drug policy would significantly raise the cost estimates of the War on Drugs•Renewed investment in community-based conservation approaches is an alterative to militarized drug control policy