As area-based marine conservation coverage expands to meet global targets, tension with fishing activities increases. While fully protected areas (FPAs) provide the largest range of long-term social-ecological benefits, their establishment has been constrained by difficulties arising from the short-term costs of protection, and associated limitations in economic incentives and in the resources required for effective implementation. Building on an existing bio-economic model for self-financed FPAs, we examine the economic and operational feasibility of establishing an ecolabel approach to balance the costs endured by fishers when implementing an FPA. Optimal increased profits can be achieved by designating the ecolabelled self-funded managed-fishing area for 20–25% of FPA. Multi-zone MPAs with a price premium derived from catch ecolabel certification inside partially protected areas surrounding FPAs provide incentives to help fishers engage into adopting sustainable fishing practices. Here we pave the way for more innovative approaches towards transformative changes for fisheries sustainability.