The effects of conservation tillage, crop residue and cropping systems on the changes in soil organic matter (SOM) and overall maize-legume production were investigated in western Kenya. The experiment was a split-split plot design with three replicates with crop residue management as main plots, cropping systems as sub-plots and nutrient levels as sub-sub plots. Nitrogen was applied in each treatment at two rates (0 and 60 kg N ha -1 ). Phosphorus was applied at 60 kg P/ha in all plots except two intercropped plots. Inorganic fertilizer (N and P) showed significant effects on yields with plots receiving 60 kg P ha -1 ? 60 kg N ha -1 giving higher yields of 5.23 t ha -1 compared to control plots whose yields were as low as 1.8 t ha -1 during the third season. Crop residues had an additive effect on crop production, soil organic carbon and soil total nitrogen. Crop rotation gave higher yields hence an attractive option to farmers. Long-term studies are needed to show the effects of crop residue, cropping systems and nutrient input on sustainability of SOM and crop productivity.