Aims Soil quality index shed light on soil health and its capacity to sustain high primary production. It also can assist decision-making in farming systems by integrating this valuable product into soil management planning. However, the currently existing models are based on rather local data, and thus, there is a lack of predictive tools to monitor soil quality. Methods We characterized soil chemical properties, and plant biomass production during 6 years in field conditions at a tropical soil. Results Our findings suggest that: 1) a consecutive green manure practice without any input of fertilizers after 6 years reduced soil quality in tropical savanna climate conditions; and 2) there are three groups of green manure considering soil quality reduction, G1 (low soil quality reduction) that comprises C. ochroleuca and N. wightii, G2 (medium soil quality reduction) that comprises B. decumbens, P. glaucum, and C. juncea, and G3 (high soil quality reduction) that comprises M. pruriens, C. ensiformis, C. spectabilis, D. lablab, and S. aterrimum. Conclusions This study highlights the importance to consider predictive models as a tool to be used in soil management. Our study also provides a deeper view about the use of green manure, and the importance to avoid the use of green manure with traits that decrease soil quality.