* 1Agricultural intensification not only alters the structure of arthropod communities, but also may affect biotic interactions by altering the availability of basal resources. We analyzed variations in stable isotope ratios (15N/14N and 13C/12C) of fertilizers, plants, prey and generalist predators in organic and conventional farming systems in a long-term agricultural experiment [DOK trial (bioDynamic, bioOrganic, Konventionell)]. Two basal resources with pronounced differences in carbon isotope signatures, wheat litter (C3 plant) and maize litter (C4 plant), were used to uncover differences in food web properties between the two farming systems (conventional versus organic). * 2Predators incorporated significantly higher proportions of carbon from wheat sources in organically managed fields, suggesting that they were more closely linked to wheat-consuming prey in this system. The δ15N values of three predaceous species were more than 2‰ greater in summer than in spring. * 3The results obtained suggest that generalist predators consumed higher proportions of herbivore prey in the organic system and that starvation and intraguild predation rates increased in some predator species with time. * 4Because the effects of farming system and sampling date on predators were species-specific, conserving a diverse natural enemy community including species with different phenologies and sensitivities to management practices may, in the long term, be a good strategy for maintaining high pest suppression throughout the growing season.