Cisco Coregonus artedi was once an important native fish in Lake Ontario; however, after multiple population crashes, the cisco stock has yet to recover to historic abundances. Rehabilitation of cisco in Lake Ontario is a fish community management objective, but the extent to which recent non-native species and pelagic food web changes have influenced cisco is not well understood. We described cisco diets in contemporary Lake Ontario following the addition and spread of non-native zooplankton species. We collected 618 cisco and processed 178 for full diet analysis in eastern Lake Ontario using mid-water trawls and bottom-set gill nets from 2016 to 2020. We found that Lake Ontario cisco were mostly zooplanktivorous, and non-native zooplankton dominated their diet during July and September. Cisco smaller than 300 mm had a more diverse diet including both native and non-native zooplankton, while cisco larger than 300 mm fed almost exclusively on non-native predatory cladocerans Bythotrephes longimanus and Cercopagis pengoi (98.9% consumed prey dry mass). We also found fish eggs, presumed to be of coregonine origin in 75% of non-empty December-collected cisco diets, suggesting eggs subsidize cisco diets when available. Juvenile round goby Neogobius melanostomus, alewife Alosa pseudoharengus and rainbow smelt Osmerus mordax were found in 2% of all analyzed non-empty stomachs. Lake Ontario cisco diet appears to be more similar to zooplanktivorous Lake Superior cisco than Lake Michigan where piscivory is prevalent. Lake Ontario cisco diets reflected zooplankton community changes indicating that non-native predatory cladocerans are now an important energy source supporting this native species.