Soils around the world are degraded due to inappropriate management practices. There is thus the necessity to find more conservationist agricultural systems. Agroforestry system is an alternative system that helps prevent land degradation while allowing continuing use of land to produce crops and livestock on a sustainable basis. Agroforestry system is a form of sustainable land use that combines trees and shrubs with crops and livestock in ways that increase and diversify farm and forest production while also conserving natural resources. This system enhances organic carbon accumulation in soils by the inclusion of cover crops and permanent vegetation, which is expected to increase the soil microbial biomass. The use of microorganisms aims at improving nutrient availability for plants. Currently, there is an emerging demand to decrease the dependence on chemical fertilizers and achieve sustainable agriculture and agroforestry. Arbuscular mycorrhizal fungi, plant growth-promoting rhizobacteria, and the association of rhizobia with leguminous plants are mutualistic symbioses of high economic importance for increasing agricultural production. The biological nitrogen fixation (BNF) process is an economically attractive and ecologically sound method to reduce external nitrogen input and improve the quality and quantity of internal resources. BNF by associative diazotrophic bacteria is a spontaneous process where soil nitrogen is limited and adequate carbon sources are available. However, the ability of these bacteria to contribute to increased crop yields is only partly a result of BNF. The successful use of legumes is dependent upon appropriate attention to the formation of effective symbioses with root nodule bacteria. An essential component for increasing the use of legumes is the integration of plant breeding and cultivar development, with appropriate research leading to the selection of elite strains of root nodule bacteria. An expansion of the utility of inoculants is also necessary to develop a broad conceptual framework and methodology that is supported by scientific arguments; it is destined to impact assessment of the use of new biological products in agriculture.