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As ubiquitous ecosystem engineers, earthworms play an important role in shaping the architecture and functioning of soil systems. However, there is limited knowledge on how earthworms modify the soil microbiome in relation to soil biogenic aggregates, hot-spots formed by earthworms, especially in agricultural systems. We investigated microbial communities in physical fractions and bulk soil from an arable field with consecutive rice - wheat cropping after manipulating earthworms and organic amendments for 13 years. Earthworms significantly enhanced soil aggregation by 33.4% across two consecutive cropping seasons. The assemblage of bacterial communities varied strongly between soil aggregate fractions and with earthworm presence, while the assemblage of fungal communities varied most with organic amendments and less between aggregate fractions. Structural equation modelling (SEM) suggests that besides direct effects on bacteria and fungi, earthworms affected bacteria indirectly via increasing soil aggregation (MWD), but mediated fungi via lowering pH, indicating that the role of soil aggregates in structuring soil bacterial communities override that of resource availability. In conclusion, results of our over-decade field experiment suggest that earthworms modify soil microbial communities primarily through mediating soil habitat architecture and affecting resource supply. • A long-term study explored earthworm impacts on aggregate-associated microbiome. • Earthworms increase soil macro-aggregates (>2 mm) formation. • Earthworms modify soil bacterial community mainly via stimulating soil aggregation. • Earthworms modify soil fungal community mainly via changing chemical properties. [ABSTRACT FROM AUTHOR]