Intercropping is an agricultural system that facilitates mutualistic and commensalist interactions among crops. The objective of this research was to test the hypothesis that intercropping with greater plant richness produces more roots that improves microbial activity, which in turn, contributes to soil physical structure that improves soil chemistry parameters, crop yield, and land use. We performed a field experiment in a randomized block design, utilizing beans (Phaseolus vulgaris), maize (Zea mays), and eggplant (Solanum melongena), under monoculture or intercropping systems. Root and soil biological, physical and chemical parameters, crop yield and land equivalent ratios were analyzed. Increased plant richness as a function of the intercropping system did not affect root and soil parameters. However, principal component analysis indicated that intercropping affected root density, mass, and length, which, in turn, contributed to the formation of soil aggregates, increased microbial activity and to the improvement of soil chemical parameters. Furthermore, as consequence of increased plant richness, the maize-beans-eggplant intercropping facilitated the positive interactions among the species and led to a Land Equivalent Ratio (LER) 60% higher than the monoculture systems. The production of roots in the crop systems, regardless of species richness, stimulates soil biological activity and affects the quality of physical structure and fertility indicators of the soil. Crop systems with higher richness of plant species promote positive interactions between plants and soil and results in a better land use ratio.