Long-term fertilization alters soil microbiological properties and then affects the soil organic carbon (SOC) pool. However, the interrelations of SOC with biological drivers and their relative importance are rarely analyzed quantitatively at aggregate scale. We investigated the contribution of soil microbial biomass, diversity, and enzyme activity to C pool in soil aggregate fractions (>5 mm, 2–5 mm, 1–2 mm, 0.25–1 mm, and 0.25 mm aggregates rather than in 0.25 mm aggregates explained 21% and 2% of C, respectively. Overall, organic matter addition could contribute to higher C storage by boosting fungal community and enzyme activity rather than by changing microbial community diversity in macro-aggregates.