Multiple anthropogenic pressures including the widespread introductions of non-native species threaten biodiversity and ecosystem functioning notably by modifying the trophic structure of communities. Here, we provided a global evaluation of the impacts of non-native species on the isotopic structure (C-13 and N-15) of freshwater fish communities. We gathered the stable isotope values (n = 4030) of fish species in 496 fish communities in lentic (lakes, backwaters, reservoirs) and lotic (running waters such as streams, rivers) ecosystems throughout the world and quantified the isotopic structure of communities. Overall, we found that communities containing non-native species had a different isotopic structure than communities without non-native species. However, these differences varied between ecosystem types and the trophic positions of non-native species. In lotic ecosystems, communities containing non-native species had a larger total isotopic niche than communities without non-native species. This was primarily driven by the addition of non-native predators at the top of the food chain that increased N-15 range without modifying the isotopic niche size of native species. In lentic ecosystems, non-native primary consumers increased N-15 range and this was likely driven by an increase of resource availability for species at higher trophic levels, increasing food chain length. The introduction of non-native secondary consumers at the centre of the isotopic niche of recipient communities decreased the core isotopic niche size, the C-13 range of recipient communities and the total isotopic niche of coexisting native species. These results suggested a modified contribution of the basal resources consumed (e.g. multi-chain omnivory) and an increase level of competition with native species. Our results notably imply that, by affecting the isotopic structure of freshwater fish communities at a global scale, non-native species represent an important source of perturbations that should be accounted for when investigating macro-ecological patterns of community structure and biotic interactions.