Purpose Interactions between plants and soil biota play an important role in maintaining the productivity and sustainability of agro-ecosystems, but mechanisms responsible for these interactions still are little understood. We investigated the growth of different faba bean genotypes in response to soil decomposer animals in monoculture and mixed cropping system. Methods In a microcosms experiment, we tested the effects of cropping system (monoculture, mixture with wheat), genotypes (S-62, S-69) and soil decomposers (earthworms, collembolans) on agronomic traits of faba bean. Trait performance and organ biomass of faba bean were evaluated after 100 and 180 days. Results Genotype S-62 performed better than S-69 for stem, leaf and flowering traits, but it was the opposite for bean biomass. Mixture with wheat reduced most agronomic traits values but not bean biomass for both genotypes. Soil decomposer animals only showed an impact on the S-69 genotype in mixture, with most agronomic traits reduced by 4.6% similar to 19.9% but bean biomass increased by 139.7%. Conclusions The effect of soil decomposer animals on bean agronomic traits varied between bean genotypes and depended on cropping system. Effects were most pronounced in the genotype allocating more resources to roots and the effects were stronger in mixed cropping systems with wheat. The more pronounced effect of soil decomposer animals in mixed cropping systems was likely due to animals increasing the competitive strength of wheat, thereby suppressing a wide range of bean agronomic traits but not bean biomass.