<p>A field experiment was conducted to investigate the effect of organic amendments on aggregate stability and yield of cassava grown on sandy soil. The experimental design used a randomized complete block with three replications. Treatments during the seven consecutive years of the 2013–2020 cropping seasons consisted of no organic amendment application (control), application of chicken manure at 6.25 t ha^− 1 (CKM1), application of chicken manure at 12.5 t ha^− 1 (CKM2), application of cassava starch waste (CSW), and cassava tails and stocks (CTS), each at 6.25 t ha^− 1. Analysis of the organic carbon (OC) fractions in the water-stable aggregate (WSA) was carried out using wet oxidation with hydrogen peroxide. The associated OC components in the WSA were investigated using Fourier transform mid-infrared spectroscopy. All organic amendments significantly improved the WSA content and associated organic carbon (OC), total nitrogen, and labile and stable OC contents compared to the control. Labile OC fractions derived from organic amendments, such as polysaccharides, had significant positive correlations with the WSA content. All organic amendments significantly increased the soil pH, nutrient elements, and cation exchange capacity (CEC) of the soil. With increasing WSA, the nutrient elements and CEC of the soil significantly increased. Consequently, most organic amendments (particularly CKM2 and CSW) significantly increased the above ground biomass and the fresh tuber and starch yields of cassava. Cassava starch manufacturing wastes, such as CSW, could be used as an organic amendment to improve aggregate stability and cassava production in this sandy soil.</p>