The importance of soil structure, packing and stability, cannot be overstated as it controls vital processes in the terrestrial environment. Physical, chemical and biological processes altogether affect the dynamics of soil structure with the biological driver being the most complex and least explored. We quantified, developing and applying advanced methods, the effect of mucilage (0.035 % w/w), the main substance in root exudates, on soil packing and stability, by micro-CT and laser granulometry (aggregate durability index), respectively. Upon mucilage addition to soils, or plant growth, soil aggregate size and aggregate stability both increased, however, the intensity varied between the soils, in the order of sandy-clay-loam > loamy-sand > clayey soils. Scanning electron microscope and X-ray diffraction measurements focusing on the smaller soil aggregates (<250 µm) and their mineralogy, bring forward their dominant role in aggregation and stabilization processes induced by mucilage. The complex effects of mucilage coupled with a physical driver, wetting and drying, on microorganism activity, were explored. Compensating microorganism activities, root mucilage consumption and self-mucilaginous polysaccharides production, most likely explain the stability steady state reached within three days. The presence of mucilage in sandy-clay-loam and clayey soils, intensified and overcame the aggregation and disaggregation induced by wetting and drying, respectively. Elucidating soil structure dynamics will enable better understanding of soil stability processes and thereby develop better strategies for soil erosion management.