The latest reform of the Common Fisheries Policy (CFP) which regulates the exploitation of fish stocks in European waters entails a move from the traditional single stock management towards Ecosystem Based Fisheries Management (EBFM). Meanwhile the Marine Strategy Framework Directive dictates that Good Environmental Status (GES) should be achieved in European waters by 2020. Here we apply an EBFM approach to the west of Scotland demersal fisheries which are currently facing several management issues: depleted stocks of cod (Gadus morhua) and whiting (Merlangius merlangus), increased predation from grey seals (Halichoerus grypus), and large bycatch of juvenile whiting by crustacean fisheries. A food web ecosystem model was employed to simulate the outcomes of applying the traditional single stock fishing mortalities (F), and management scenarios which explored F ranges in accordance with the CFP. Ecosystem indicators were calculated to assess the performance of these scenarios towards achieving GES. Our results highlight the importance of considering prey-predator interactions, in particular the impact of the top predators, cod and saithe (Pollachius virens), on juvenile cod and whiting. The traditional single stock approach would likely recover cod, but not whiting. Exploring the F ranges revealed that a drastic reduction of juvenile whiting bycatch is necessary for the whiting stock to recover. Predation from grey seals had little impact overall, but did affect the timing of cod and whiting recovery. With the exception of whiting, little difference was observed between the single stock scenario, and the best scenario identified towards achieving GES. The findings advocate for the use of ecosystem modelling alongside the traditional single stock assessment models used for tactical decision making in order to better inform fisheries management.