Global warming is altering the composition and functioning of both terrestrial and aquatic ecosystems. Most research has focussed on direct effects of warming on species and their population dynamics, while less is known about indirect effects through species interactions. Trophic cascades are especially likely to influence the effects of warming given that trophic levels differ in their response to warming because of differences in metabolism and vital rates such as growth and reproduction. We investigated if the top-down effect of a common mesopredator, the threespine stickleback, alters the impact of warming on a Baltic Sea food web. We manipulated both temperature and the presence of stickleback in mesocosms, and found the stickleback to alter the impact of warming on lower trophic levels. This was through increased consumption of herbivores that exceeded the rate at which the herbivore population could grow under higher temperature, which in turn increased algae biomass compared to a scenario without stickleback, but not compared to conditions under normal temperature. Thus, the mesopredator increased the transfer of biomass to higher trophic levels of the food web when temperature was increased. This stresses the importance of considering the impact of warming on multiple trophic levels and their interactions. Failing to consider differences in responses among trophic levels and the impact this has on their interactions can result in faulty conclusions about the impact of warming on ecosystems.