The spatial distribution of soil microorganisms in soil structure remains poorly known, despite its functional importance. Here, we analyzed the spatial distribution of microorganisms able to mineralize different organic substrates, i.e. glucose, leucine, 2,4-D and its metabolite 2,4-DCP, among aggregates of different sizes, from 2-3 mm down to 0.05-0.2 mm. For this, we used 14C labeled substrates and a miniaturized incubation system that allows to trap the 14C-CO2 evolved from separately incubated individual aggregates. The evolved 14C-CO2 was quantified using a phosphore imager. 96 different aggregates were processed for each size class and each substrate. We observed a large heterogeneity of the mineralization potential between individual aggregates of a given size class. The heterogeneity tended to increase as aggregate size decreased. The heterogeneity was also larger for xenobiotic substrates, i.e. 2,4-D and 2,4-DCP degraded by a small community, than for natural ubiquitous substrates, i.e. glucose and leucine.