An integrated ecosystem model including fishing and the impact of rising temperatures, relative to species’ thermal ranges, was used to assess the cumulative effect of future climate change and sustainable levels of fishing pressure on selected target species. Historically, important stocks of cod and whiting showed declining trends caused by high fisheries exploitation and strong top-down control by their main predators (grey seals and saithe). In a no-change climate scenario these stocks recovered under sustainable management scenarios due to the cumulative effect of reduced fishing and predation mortalities cascading through the food-web. However, rising temperature jeopardised boreal stenothermal species: causing severe declines in grey seals, cod, herring and haddock, while eurythermal species were not affected. The positive effect of a higher optimum temperature for whiting, in parallel with declines of its predators such as seals and cod, resulted in a strong increase for this stock under rising temperature scenarios, indicating a possible change in the contribution of stocks to the overall catch by the end of the century. These results highlight the importance of including environmental change in the ecosystem approach to achieve sustainable fisheries management.