To understand ecosystems, an integrative approach combining functional ecology and community ecology is required. Nutrient cycling is a good example since it links each organism to the major flows of materials in ecosystems. Together with the demographic processes governing the mortality of organisms (and hence their nutrient losses) such as self-regulation, nutrient recycling has a major impact on ecosystem dynamics and stability. By considering stochastic perturbations in the vicinity of the equilibrium affecting the top species in a food chain, we assessed stability based on the temporal variability in the different compartments of the food chain for different recycling efficiencies and self-regulation intensities. Our results show that nutrient cycling always has a destabilising effect on perturbed species, while lower trophic levels are stabilised or destabilised depending on their trophic distance from the perturbed species. Thus, for species at odd distances from the top species, nutrient cycling is stabilising, whereas for species at even distances, nutrient cycling is destabilising. Self-regulation generally stabilises systems, unless its effects are too strong. Finally, nutrient cycling and self-regulation have opposite effects because nutrient cycling dampens the stabilising effect of self-regulation. Considering these two phenomena together is necessary to assess the effects of perturbations on species dynamics and thus to understand the overall response of ecosystems in the context of global changes.