Due to common agricultural practices, biodiversity is lost, soil is degraded and nutrients are leached collectively leading to lower crop productivity. To increase sustainability in agricultural systems, farmers use cover crops to reduce nutrient losses, reduce pests, increase soil organic matter, increase soil biota, etc. The functional traits (C:N ratio, nitrogen fixing, rooting depth, microbial association) differ between cover crop species. It is hypothesized that combining plant species with different, complementary traits have a positive effect on soil functioning. Studies in natural ecosystems have shown that plant diversity improves soil microbial diversity leading to enhanced ecosystem functioning. In a pot experiment, residues of cover crop monocultures (three monocultures: radish, vetch and oat) and mixtures (three species mixture of radish, vetch and oat and a 15 species mixture) were mixed with soil. During cover crop decomposition, fungal biomass, microbial functional diversity, greenhouse gas emissions and soil nutrients were measured over time. C:N ratio of the cover crop (mixtures) is an important variable in explaining CO2 and N2O emissions. Mixtures of cover crops only showed reduced N2O and CO2 emissions compared to monocultures at the start of the experiment. Adding nitrogen to the cover crop treatment with the highest C:N ratio (oat) did increase N2O emissions, but not CO2 emissions. Nitrogen fertilization alone might be not sufficient to increase decomposition in oat. Fungal biomass increased for all treatments compared to a control without addition of cover crop residues but there were no additional effects of cover crop mixtures. Interestingly, soil microbial functional diversity, measured with Biolog ECO plates, was significantly higher in cover crop mixtures as compared to monocultures. Residue mixtures might increase niches for microbes in the soil by adding higher diversity of substrates or by changing soil physico-chemistry by different rooting patterns that can lead to increased functional diversity.