Overfishing of large predatory fish populations has resulted in lasting restructurings of entire marine food webs worldwide, with potential immense socio-economic consequences. Fortunately, some degraded ecosystems have started to show signs of regeneration. A key challenge for resource management is to anticipate the degree to which regeneration is possible, given the multiple threats ecosystems face. Here, we show that under current hydroclimatic conditions, complete regeneration of a heavily altered ecosystem –the Baltic Sea as case study– would not be possible. Instead, as the ecosystem regenerates it moves towards a new ecological baseline. This new baseline is characterized by lower and more variable biomass of the commercially important Atlantic cod, even under very low exploitation rates. Consequently, societal costs increase due to higher risk premium caused by increased uncertainty in biomass and reduced consumer surplus. Specifically, the combined economic losses amount to about 120 million € per year, which equals half of today’s maximum economic yield for the Baltic cod fishery. Our analyses suggest that shifts in ecological and economic baselines, in combination with increased biomass variability, lead to higher economic uncertainty and costs for exploited ecosystems, in particular under climate change.Kiel Cluster of Excellence 'Future Ocean