An understanding of the concomitant effects of elevated atmospheric CO₂ concentrations and drought on soil C cycling in agricultural systems is limited. We investigated the effects of elevated CO₂ (eCO₂) and drought on soil organic matter (SOM) dynamics and soil microbial distribution in a soybean system across soil environments (i.e., rhizosphere and bulk soil) and SOM fractions (coarse particulate organic matter (cPOM; >250 mm), microaggregate (53-250 mm), and silt-and-clay fraction (<53 mm)) at the Soybean Free Air Concentration Enrichment (SoyFACE) experiment in Illinois, USA. To study the distribution of microorganisms across soil environments and in the microaggregates, we quantified the total bacterial (16S rRNA) and denitrifier (nosZ) genes. We were unable to detect any significant effects of the different treatments on soil C and N concentrations either in the whole soil or in the SOM fractions within the same soil environment. Soil C and N concentrations in the microaggregates were significantly higher in the bulk soil than in the rhizosphere, whereas the opposite effect was observed for the silt-and-clay and cPOM fractions. The mass of microaggregates was the highest under drought in both rhizosphere and bulk soil. The quantification of 16S rRNA and nosZ community sizes indicated that drought increased the abundance of those genes inside microaggregates compared to ambient conditions of soil moisture, whereas no effects were observed in the whole soil. This suggests that microagregates, besides the fundamental role in C sequestration, can promote microbial growth even under environmental stresses such as drought.