A vessel-based bio-economic model (IAM) is presented and applied to the Bay of Biscay sole fishery to investigate alternative quota management systems from a multi-criteria perspective. For this study, the model integrates several institutional arrangements related to catch share management. The current French co-management system with non-transferability of quota is compared to an alternative ITQ system in a context of transition to maximum sustainable yield (MSY). Trade-offs between ecological and socio-economic impacts are highlighted and the effectiveness of governance scenarios is discussed in regard to the challenge of capacity adjustment. Results emphasize that the introduction of ITQ is expected to reduce by 40% the number of vessels in the fishery. While effectively mitigating the economic impacts of the transition phase to MSY, ITQs are also expected to significantly increase the fishing effort by trawlers, which may cause ecological concerns. The scenarios tested also include the simulation of a decommissioning scheme where subsequent decommissioned vessels are significantly different from the vessels that would lease out their quotas in an ITQ system, resulting in differentiated ecological and socio-economic impacts between scenarios.