The Faroe Islands are currently struggling to find their feet in a new context of globalisation and changing international requirements on fishery management best practices, as exemplified by United Nations protocols and agreements. We introduce the Faroese fisheries effort management system for cod, haddock and saithe, which represents an innovative attempt to tackle the challenges of mixed fisheries by means of a combination of total allowable effort implemented through days-at-sea and extensive use of closed or limited access areas. Subsequently, we present and discuss controversies concerning the system’s ability (or lack thereof) to achieve a level of fishing effort that produces long-term sustainability. Over the years the system has proved able to evolve and overcome challenges, and the Faroe Islands are currently considering adding a proper fisheries management plan to the system to achieve fishing at maximum sustainable yield. However, finding support for this plan presents a challenge due particularly to an enduring gap between the perspectives of scientists and actors in the catching sector. Finally, we outline some actions that could be taken to reduce the gap and hence facilitate reform of the system: 1) integration of the consultative/advisory process; 2) obtaining tailor-made advice for the Faroese effort management system from the relevant scientific body; 3) establishment of a transparent mechanism for monitoring and regulating fishing effort; 4) clarifying the efficacy of the prevalent system of closed areas.