Abstract <p>This paper examines the application of focused ion beam scanning electron microscopy (FIB-SEM) for investigating the submicron structure of soil aggregates. The object of the study was migratory-micellar chernozem from the Central Chernozem Reserve. A comparative analysis was performed between images obtained using FIB-SEM and X-ray computed tomography. The study addresses whether investigations based on FIB-SEM can complement analyses conducted using computed tomography alone. FIB-SEM has demonstrated the capability to identify pores with radii smaller than 1 μm, which are inaccessible to tomography, as well as to reveal organic inclusions and specific pore morphotypes (crack-like, elongated, and irregular) that reflect physicochemical processes at the nanoscale, i.e., for pores smaller than one micrometer. However, the limited field of view and the high labor intensity of image segmentation reduce the representativeness of this method. The results confirm the applicability of FIB-SEM as a complementary tool to conventional tomography in studies of soil structure, which opens prospects for organic matter analysis and for refining the mechanisms of structure formation at the submicron level.</p>