Population dynamics depend on trophic interactions that are affected by climate change. The rise in sea temperature is associated with the disappearance of sea ice in the Arctic. In the Arctic part of the Barents Sea, Atlantic cod, capelin and polar cod are three fish populations that interact and are confronted with climate-induced sea ice reductions. The first is a major predator in the system, while the last two are key species in Arctic and sub-Arctic ecosystems, respectively. There are still many unknowns regarding how predicted environmental change may influence the joint dynamics of these populations. Using time series from a 32 year long survey, we developed a state-space model that jointly modelled the dynamics of cod, capelin and polar cod. Using a hindcast scenario approach, we projected the effect of reduced sea ice on these populations. We show that the impact of sea ice reduction and concomitant sea temperature increase may lead to a decrease of polar cod abundance at the benefit of capelin but not of cod which may decrease, resulting in strong changes in the food web. Our analyses show that climate change in the Arcto-boreal system can generate different species assemblages and new trophic interactions, which is the knowledge needed for effective management measures.