Fisheries management in marine protected areas (MPAs) aims to preserve the health of ecosystems and the fisheries they support. Fisheries actions in MPAs are selected from a diverse array of management tools and implemented under the assumption that they are not deleterious and do not impede conservation efforts. However, proper evaluations are needed to assess the effectiveness of management strategies. We analyzed 7 yr changes in the structure of benthic communities in the MPA in Bahía Independencia, one of the most productive coastal regions worldwide and part of the Humboldt Current upwelling system off Peru. Owing to the high productivity and the limited resource use allowed, we predicted that environmental variability rather than small-scale fishing activities would drive community changes. We found a significant unidirectional change in benthic community structure of the Bahía Independencia that was strongly associated with the continuous extraction of a few benthic species, with little influence of environmental factors. We suggest that the fishing of filter feeding bivalves and crabs is linked to the disturbances to macroalgae and associated fauna and probably to the release of top-down effects, which led to ~43% reduction in biomass of the whole benthic community. Our findings indicate that establishing MPAs and implementing standard fisheries management strategies in this productive coastal area may not be enough to guarantee the conservation and sustainable use of their resources. Managers should be able to implement site-specific management actions that take into account the full array of interactions between humans, biological communities and particularities of the physical setting.