Previous studies indicated that the quality of tropical composts is poorer than that of composts produced in temperate regions. The aim of this study was to test the type of manure, the use of co-composting with green waste, and the stabilization method for their ability to improve compost quality in the tropics. We produced 68 composts and vermicomposts that were analysed for their C, lignin and NPK contents throughout the composting process. Bayesian networks were used to assess the mechanisms controlling compost quality. The concentration effect, for C and lignin, and the initial blend quality, for NPK content, were the main factors affecting compost quality. Cattle manure composts presented the highest C and lignin contents, and poultry litter composts exhibited the highest NPK content. Co-composting improved quality by enhancing the concentration effect, which reduced the impact of C and nutrient losses. Vermicomposting did not improve compost quality; co-composting without earthworms thus appears to be a suitable stabilization method under the conditions of this study because it produced high quality composts and is easier to implement.