The Bay of Biscay anchovy fishery system has undergone important transformations following a closure from 2005 to 2010. Through a multidisciplinary and systemic approach, combining analyses of fisheries and market data with interviews with key stakeholders, we analyze adaptive responses of the main system components in France and Spain, considering how the fishing sector and fishery management institutions have adapted to changes. Focusing on the question “what has been lost and gained following the collapse?”, we find that while the anchovy stock has recovered, the fishery system has not returned to its pre-collapse status with important socio-economic features having been lost. We highlight the need for holistic consideration of multiple system components and diverse stakeholders’ perspectives. The perceived losses and gains from the anchovy fishery collapse and aftermath are found to vary across the players in the fishery system, depending as well on the management objectives and scales being considered. Such retrospective analysis can serve as a basis for understanding the long-term responses to social-ecological changes in fisheries, and identifying the role of governance mechanisms in supporting adaptations that maintain sustainable fishery systems in the face of future potential shocks.