Large mammals play key roles in tropical forests but are currently threatened worldwide. A big question is to what degree protected areas are effective in maintaining these large mammals. Here, we assess whether protected forests effectively protect large mammals along the Isthmus of Panama, a bottleneck in the Mesoamerican Biological Corridor that is essential for species migration and gene flow, but is increasingly fragmented. During 2005-2016, we used camera traps to survey terrestrial mammals in 17 protected forests scattered across Panama. We determined occupancy rates for the nine largest extant species, which differ in their sensitivity to disturbance. Based on 26,000 trap days from > 500 camera trap stations, we found that most protected forests had impoverished, structurally simplified mammal communities, with few or no apex predators and large terrestrial frugivores. Occupancy analysis revealed consistent patterns of avoidance of human disturbance and forest edges by Tapirus bairdii and Tayassu pecari, which are heavily hunted, and concentration at higher elevations. Only in our most remote site, far away from any anthropogenic activity, did these species still occur in lowland areas. Carnivores, in contrast, when present at a site, were less affected by anthropogenic factors. Our findings indicate that the protected areas of Panama are not effective in maintaining the entire mammal community, and show clear signs of anthropogenic declines in abundance and shifts in habitat use of large terrestrial mammals. Our study also suggests a lack of connectivity between protected areas. We propose recommendations to improve mammal conservation in Mesoamerica.