Eastern Baltic cod is an example of a fish stock where fishing pressure has substantially declined after decades of intensive exploitation. However, in contrast to the expected improvements in stock status, stock productivity has concurrently declined to a historic low level. Targeted fisheries for the eastern Baltic cod were recently banned. However, at present low growth and high natural mortality, the stock biomass is projected to remain low, even in the absence of fishing. Thus, the future development in this stock and its potential recovery are largely dependent on ecosystem drivers likely contributing to the presently poor state of the cod stock (e.g. oxygen conditions, spatial distribution of prey species, abundance of marine mammals). Some of these ecosystem drivers and associated impacts on cod may be possible to influence by management measures, which are however not straightforward to implement. Moreover, scientific knowledge to guide management decisions in a complex ecosystem context is lagging behind. The Baltic cod case exemplifies the complexity of questions emerging for management as well as scientific advice under rapidly changing ecosystem conditions, where traditional fisheries management alone may have a limited potential to rebuild the stock.