Most worldwide fish stocks are overexploited, and so exploited beyond the Maximum Sustainable Yield (MSY) and the Maximum Economic Yield (MEY). Not exploiting fisheries resources at MSY or MEY leads to the loss of production and rents from the fisheries. A large part of the EU fisheries are managed based on single species stock assessments; however, in reality, most species are caught together with other species and by different fleets. In multi-species and multi-fleet fisheries, single species assessments, and consequently MSY and MEY reference points, are often not valid, and so the catch recommendations. In this paper it is investigated the MSY and MEY estimation in multi-species and multi-fleet fisheries in comparison to single species assessments. Analyses are applied to the Bay of Biscay demersal fishery using the IAM bio-economic model. The impact of exploiting at MSY and MEY on the optimal effort allocation between fleets with different exploitation patterns and economic structures is analyzed. When accounting for the multi-species nature of the fishery, MSY landings are 0.4% to 2.7% lower than the single species simulations estimates. When accounting for the multi-fleet nature of the fishery, MSY landings are 27.2% to 30.2% higher than the single-fleet estimates. When considering the multi-fleet characteristics, MEY landings are 6.6% higher and profits are 66.5% higher than in the single-fleet simulation. Optimal effort at MEY is lower than at MSY, but when accounting for multi-fleet the optimal effort decreases for some fleets while increases for gillnetters. The results also provide an estimation of the profits at MEY (or costs of not being at MEY). Profits can be then up to 10.7 times larger than the current profits (256 million Euros compared to the current 24 million Euros).