Mixed cropping, crop breeding and soil biodiversity all serve as promising strategies for the management of agroecosystems, but empirical evidence for their synergies and trade-offs remains little explored. Here, we studied the effects of two main soil decomposers, collembolans and earthworms, on 15N uptake from organic residues, crop production, resource allocation and shoot-root C/N ratio of two bean genotypes (S-62 and S-69) in monoculture and mixture with wheat in a microcosm experiment. Soil decomposers mainly increased the productivity of wheat and little that of beans, but their effects on wheat varied with bean genotype. Earthworms increased the biomass of reproductive (+231%) and vegetative (+36%) organs as well as that of roots (+56%) of wheat in mixtures with S-62. Conversely, neither collembolans nor earthworms significantly affected wheat biomass when cultivated with S-69. Effects of decomposers on crop C/N ratio were pronounced in beans, but varied between cropping systems as well as between genotypes. In monoculture, collembolans decreased shoot C/N ratio of S-69 by 10%, whereas in mixture they increased it by 11% in S-62 irrespective of the presence of earthworms. 15N uptake by crop species was mainly affected by mixed cropping and earthworms; mixed cropping generally reduced the uptake of litter 15N by both crops, whereas earthworms generally increased it. The results document that soil decomposers differentially affect different genotypes of crops in particular in mixture and indicate that wheat benefits more from decomposers than beans. Both the non-uniform and complementary effects of soil decomposers on crop performance suggest that maintaining soil biodiversity may help in establishing sustainable cropping systems and this may be particularly important in mixture. The differential response of different genotypes to soil decomposers suggests that breeding programs targeting at establishing plant genotypes responsive to decomposer-mediated changes in plant performance may help in the establishment of sustainable monoculture but particularly mixed cropping systems in future.