The relative importance of different binding mechanisms and associated biological binding agents on aggregate stability is still unclear. The aim of this study was to evaluate the role of various aggregate binding agents during the decomposition of cauliflower residues, wheat straw, cattle manure and poultry woody compost. We measured aggregate stability, hot-water extractable polysaccharide, C mineralization, fungal and microbial biomass dynamics in an amended silt loam soil, under controlled conditions. Soil aggregate stability was measured using three methods involving fast wetting, slow wetting and mechanical breakdown. Aggregate stability to slow wetting followed the same dynamics as C mineralization and was well correlated with polysaccharide content for cauliflower residues and wheat straw. This relationship is in agreement with the hypothesis that the rapid microbially induced improvement in aggregate stability that follows fresh organic residue additions at least partly involves labile polysaccharides. The transient increase in the two other types of stability was not directly related to C mineralization dynamics and seemed to be influenced by fungal hyphal length. Fungi would provide resistance to mechanical breakdown and slaking. The dynamic behaviour of biological binding agents was only partly explained by the initial quality of the organic materials, as characterized by Van Soest proximal fractionation.