Non-native species are considered a major global threat to biodiversity, and their expansion to new ecosystems has recently increased. However, the effect of non-native species on ecosystem functioning is poorly understood, especially in hyperdiverse tropical ecosystems of which long-term studies are scarce. We analyzed the relationship between richness, biomass, and beta-diversity of non-native and native fishes during 16 years in five hyperdiverse tropical shallow lakes. We further elucidated how an observed increase in the proportion of richness, biomass, and beta-diversity of non-native over native fishes affect crucial multifunctional processes of lakes (decomposition, productivity). We found a general positive relationship between the richness and biomass of non-native and native fishes. However, the slope of this relationship decreased continuously with time, displaying an increase in non-native species richness and a decrease in native species richness over time. We also detected a negative relationship between the beta-diversity of non-native and native fishes over time. Moreover, the increase in the non-native:native ratio of species richness, biomass, and IS-diversity over time decreased ecosystem multifunctionality. Our results suggest that non-native fishes caused a homogenization of the native fish species over time, resulting in impoverishment of ecosystem multifunctionality; in part because nonnative fishes are less productive than native ones. Therefore, focus on long-term effects and use of multiple biodiversity facets (alpha- and beta-diversity) are crucial to make reliable predictions of the effects of non-native fish species on native fishes and ecosystem functioning. (C) 2021 Elsevier B.V. All rights reserved.