As Arctic sea ice deteriorates, more light enters the ocean, causing largely unknown effects on the ecosystem. Using an autonomous biophysical observatory, we recorded zooplankton vertical distribution under Arctic sea ice from dusk to dawn of the polar night. Here we show that zooplankton ascend into the under-ice habitat during autumn twilight, following an isolume of 2.4 × 10−4 W m−2. We applied this trigger isolume to CMIP6 model outputs accounting for 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 habitat could be reduced by up to one month, depending on geographic region. This will impact zooplankton winter survival, the Arctic foodweb, and carbon and nutrient fluxes. These findings highlight the importance of biological processes during the twilight periods for predicting change in high-latitude ecosystems.