We studied the biochemical and biophysical processes of carbon sequestration in an intensive agroforestry system on two soils (Feralsol – Luero; Arenosol – Teso) in W. Kenya to elucidate the mechanisms associated with long-term carbon storage. Specifically, we looked at a top-down model (macro-aggregates form around organic matter particles and micro-aggregates form within the macro-aggregates) and a bottom-up model (micro-aggregates form independently and are incorporated into macro-aggregates) of soil aggregate formation. Soil samples were collected from experiments on improved tree fallows using different species and two tillage treatments; water-stable aggregates were extracted and sorted into three size classes: macro-aggregates (> 212 μm), meso-aggregates (53–212 μm) and micro-aggregates (20–53 μm). Organic matter characterization of each fraction was based on 13C isotope abundance, Fourier transform infrared (FTIR) spectroscopy and the abundance of polysaccharides. Improved fallows increased soil C by 0.28 and 0.26 kg m 2 in the top 20 cm of the soil profile in Luero and Teso, respectively. Tillage altered the distribution of aggregates among size classes. Changes in the δ 13C signature in each fraction indicated that more of the new carbon was found in the macro-aggregates (35–70%) and meso-aggregates (18–49%) in Luero and less (9–17%) was found in the micro-aggregates. In Teso, about 40–80% of the new aggregate C was found in the meso-aggregates, 14–45% was found in the micro-aggregates and only 4–26% was found in the macro-aggregates. The meso-aggregates and macro-aggregates to a lesser extent, in both sites, were enriched in carboxylic-C and aromatic-C, indicating the importance of OM decomposition and plant-derived C in the stabilization of larger aggregates, supporting the top-down model of aggregate formation. Microbially derived polysaccharides play a leading role in the formation of stable micro-aggregates and carboxylic-C promotes stabilization through surface occlusion. This bottom-up process is essential to promote long-term carbon sequestration in soils. Additionally, the micro-aggregates at both sites were enriched in polysaccharides and had elevated ratios of galactose + mannose:arabinose + xylose than the other aggregate fractions, indicating the importance of microbial processes in the formation of stable micro-aggregates and supporting the bottom-up model.