Background and aims: Crop straw and it derived biochar are both promising to improve soil fertility and structure. However, the contribution of these amendments to microbial biomass and aggregate formation, as well as carbon (C) and nitrogen (N) stabilization within aggregates is lacking. Methods: Maize straw that was labelled with 13C and 15N or its biochar (produced at 400 °C) were added to soil to quantify the incorporation of C and N into dissolved organic matter, microbial biomass, and aggregates throughout lab incubation. Results: After 20 days of incubation, 48% of microbial biomass C (MBC) and 18% of microbial biomass N (MBN) was derived from straw. In contrast, biochar contributed 4% to the MBC pool, with only a trace contribution to MBN. These contributions were reflected in the dissolved organic matter C and N pools. Soil aggregation (mean weight diameter) was 14% greater amended with straw than with biochar within the first 100 days, but without differences thereafter. Because the straw-derived binding agents for aggregation are short-lived, their effects on aggregate formation disappeared after 100 days resulting in a similar impact as that found in soil with biochar. Larger amounts of straw-derived C and N were occluded within aggregates compared to biochar. Conclusion: The amendments of soil with straw and biochar affected microbial processing, reflected in the uptake of C and N into microbial biomass, dissolved organic matter and aggregates. We conclude that straw has a short-term effect on aggregation, while biochar has limited impact on aggregation.