The ecosystem effects of all commercial fishing methods need to be fully understood in order to manage our marine environments more effectively. The impacts associated with the most damaging mobile fishing methods are well documented leading to such methods being removed from some partially protected areas. In contrast, the impacts on the ecosystem from static fishing methods, such as pot fishing, are less well understood. Despite commercial pot fishing increasing within the UK, there are very few long term studies (> 1 year) that consider the effects of commercial pot fishing on temperate marine ecosystems. Here we present the results from a controlled field experiment where areas of temperate reef were exposed to a pot fishing density gradient over 4 years within a Marine Protected Area (MPA), simulating scenarios both above and below current levels of pot fishing effort. After 4 years we demonstrate for the first time negative effects associated with high levels of pot fishing effort both on reef building epibiota and commercially targeted species, contrary to existing evidence. Based on this new evidence we quantify a threshold for sustainable pot fishing demonstrating a significant step towards developing well-managed pot fisheries within partially protected temperate MPAs.