Abstract Aquatic ecosystems are tightly linked to terrestrial ecosystems by exchanges of resources, which influence species interactions, community dynamics and functioning in both ecosystem types. However, our understanding of how this coupling responds to climate warming is restricted to temperate, boreal and arctic regions, with limited knowledge from tropical ecosystems. We investigated how warming aquatic ecosystems impact cross‐ecosystem exchanges in the tropics, through the export of aquatic resources into the terrestrial environment and the breakdown of terrestrial resources within the aquatic environment. We experimentally heated 50 naturally assembled aquatic communities, contained within different‐sized tank‐bromeliads, to a 23.5–32°C gradient of mean water temperatures. The biomass, abundance and richness of aquatic insects emerging into the terrestrial environment all declined with rising temperatures over a 45‐day experiment. Structural equation and linear mixed effects modelling suggested that these impacts were driven by deleterious effects of warming on insect development and survival, rather than being mediated by aquatic predation, nutrient availability or reduced body size. Decomposition was primarily driven by microbial activity. However, total decomposition by both microbes and macroinvertebrates increased with temperature in all but the largest ecosystems, where it decreased. Thus, warming decoupled aquatic and terrestrial ecosystems, by reducing the flux of aquatic resources to terrestrial ecosystems but variably enhancing or reducing terrestrial resource breakdown in aquatic ecosystems. In contrast with increased emergence observed in warmed temperate ecosystems, future climate change is likely to reduce connectivity between tropical terrestrial and aquatic habitats, potentially impacting consumers in both ecosystem types. As tropical ectotherms live closer to their thermal tolerance limits compared to temperate species, warming can disrupt cross‐ecosystem dynamics in an interconnected tropical landscape and should be considered when investigating ecosystem‐level consequences of climate change.