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This study aimed to quantify the effect of tillage, crop rotation and crop residue management on aggregate stability, binding agents and the resulting aggregate microstructure in a sweet sorghum-based cropping system in a low organic carbon soil. Two tillage levels; no-till (NT) and conventional tillage (CT), two crop rotations, i.e., sweet sorghum-grazing vetch-sweet sorghum (S-V-S) and sweet sorghum-fallow-sweet sorghum (S-F-S) and three crop residue retention levels, i.e., 0%, 15 % and 30 % were tested. The study showed that tillage is the main factor that influences soil aggregation followed by residue management. The study also demonstrated that aggregate stability is linked to aggregate microstructure and regular pores are dominated in degraded soils with low SOC.