As Arctic sea ice deteriorates, more light enters the Arctic Ocean, causing largely unknown effects on the ecosystem. A novel autonomous bio-physical observatory provided the first record of zooplankton vertical distribution under sea ice drifting across the Arctic Ocean from dusk to dawn of the polar night. Its measurements revealed that zooplankton ascend into the under-ice layer during autumn twilight, following an isolume of 5.5 10-4 W m-2. We applied this trigger isolume to IPCC models enabled to incorporate incoming radiation after sunset and before sunrise of the polar night. The models project that, in about three decades, the total time spent by zooplankton in the under-ice layer will be reduced by up to one month, depending on geographic region. This will impact zooplankton winter survival, the Arctic foodweb, carbon- and nutrient fluxes. These findings highlight the importance of processes in the twilight periods for predicting change in high-latitude ecosystems.