When species spread into new regions, competition with native species and predatory–prey relationships play a major role in whether the new species can successfully establish itself in the recipient food web and become invasive. In aquatic habitats, species with a metagenetic life cycle, such as the freshwater jellyfish Craspedacusta with benthic polyps and planktonic medusae, have to meet the requirements of two distinct life stages occurring in two habitats with different food webs. Here, we examined the trophic position of both life stages, known to be predatory, and compared their niches with those of putative native competitors using stable isotope analysis. We found that δ13C and δ15N signatures of medusae overlapped with those of co-occurring Chaoborus larvae and juvenile fish (Rutilus rutilus) in a well-studied lake, implying high competition with these native predators. The comparison of δ15N signatures of Hydra and Craspedacusta polyps in four additional lakes revealed their similar trophic position, matching their predatory lifestyle. However, their δ13C signatures differed not only across all four of the lakes studied but also within one lake over time, suggesting a preference for pelagic or benthic food sources. We conclude that invasive and native polyps differ in their niches due to different food spectra, which favors the invasion success of Craspedacusta.