Ecosystems are linked to neighbouring ecosystems not only by dispersal, but also by the movement of subsidy. Such subsidy couplings between ecosystems have important landscape-scale implications because perturbations in one ecosystem may affect community structure and functioning in neighbouring ecosystems via increased/decreased subsidies. Here, we combine a general theoretical approach based on harvesting theory and a two-patch protist meta-ecosystem experiment to test the effect of regional perturbations on local community dynamics. We first characterized the relationship between the perturbation regime and local population demography on detritus production using a mathematical model. We then experimentally simulated a perturbation gradient affecting connected ecosystems simultaneously, thus altering cross-ecosystem subsidy exchanges. We demonstrate that the perturbation regime can interact with local population dynamics to trigger unexpected temporal variations in subsidy pulses from one ecosystem to another. High perturbation intensity initially led to the highest level of subsidy flows; however, the level of perturbation interacted with population dynamics to generate a crash in subsidy exchange over time. Both theoretical and experimental results show that a perturbation regime interacting with local community dynamics can induce a collapse in population levels for recipient ecosystems. These results call for integrative management of human-altered landscapes that takes into account regional dynamics of both species and resource flows.