The productivity and sustainability of many tropical agricultural systems must be increased to meet sustainability requirements to prevent deforestation of new non-agricultural areas. The availability and uptake efficiency of crop nutrients are fundamental considerations for any attempt to achieve this increase in productivity. We hypothesised that leguminous residues modify soil attributes through chemical and biological changes that affect plant growth and the long-term sustainability of agroecosystems in humid tropical regions. The present study aimed to determine the effects of leguminous biomass on the variations of soil organic matter fractions and soil basic cation contents and to evaluate the effects of these changes on the proportions of soil phosphorus (P) in different pools in a cropping system. A randomised block design with four replications and the following treatments was used for the modified alley cropping: Leucaena + Clitoria (L + C); Leucaena + Gliricidia (L + G); Leucaena + Acacia (L + A); Gliricidia + Acacia (G + A); Gliricidia + Clitoria (G + C), and no residues (NR). Our results confirmed the positive effects of the long-term application of leguminous biomass on those soil attributes that are the main drivers of the sustainability of tropical agroecosystems. However, such effects can differ depending on the biomass quality used. Indeed, the biomass of lower quality was more efficient in redirecting the fluxes of P towards the organic P pool, decreasing the less available Pi fractions. While the use of high-quality biomass from leucaena + gliricidia was superior to increase the stabilised carbon fraction in association with basic cations content. Ultimately, it can be concluded that to prevent cultivated land degradation and to avoid deforestation of new areas in the Amazonian periphery, production and application of high-quality biomass is an adequate strategy.