Marine coastal ecosystems are among the most exposed to global environmental change, with reported effects on species biomass, species richness and length of trophic chains. By combining a biologically informed food-web model with information on anthropogenic influences in 701 sites across the Caribbean region, we show that fishing effort, human density and thermal stress anomaly are associated with a decrease in local food-web persistence. The conservation status of the site, in turn, is associated with an increase in food-web persistence. Some of these associations are explained through effects on food-web structure and total community biomass. Our results unveil a hidden footprint of human activities. Even when food webs may seem healthy in terms of the presence and abundance of their constituent species, they may be losing the capacity to withstand further environmental degradation.