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The formation of soil aggregates is related to the stability of soil organic carbon, which distinguishes the living conditions of microbial communities in different micro-niches. Here, we investigated fungal and bacterial community structure, networks, biomass and respiration in individual micro-niches between and within soil aggregates using seven different chronosequences (both primary and secondary successions from pioneer stages to well-developed ecosystems) on a European-scale gradient from a maritime climate in Belgium to a more continental climate in Hungary. We showed that geographical location was the most important factor (74% for bacterial community, 53% for fungal community) affecting microbial community composition, while soil aggregates (5% for bacterial community and 12% for fungal community) were the second most important factor followed by age of succession and vegetation. Moreover, aggregates (52%) were the most important factor influencing the biomass of major microbial groups, followed by location (37%) and age of succession (6%). Interestingly, macro-aggregates had less interconnected microbial networks and low microbial respiration rates compared to other aggregate sizes. We therefore hypothesize that the embedding of organic particles in the mineral matrix of macro-aggregates is a crucial point in microbial community organization, as evidenced by microbial community connectivity and microbial respiration. Our results demonstrate the importance of soil aggregates for microbial community organization and soil carbon stabilization. • Soil aggregates were an important determinant of microbial community structure and biomass. • Microbial community networks were less interconnected in macro-aggregates over wide areas. • Macro-aggregates had lower microbial respiration rates compared to the other aggregates. • Microbial community network degrees were correlated with microbial respiration. [ABSTRACT FROM AUTHOR]