Soil microorganisms plays an important role on plant development and the homogenization of soil microbiome is agri-environmental harmful. It is essential that agricultural practices are carried out taking soil microbiome preservation in consideration. Agroforestry systems are one of the most environmentally friendly agrosystems and its plant diversity influence directly the soil microbiome diversity. In addition, many technologies have been developed and used by applying inoculants in agriculture. However, most of the inoculants are developed with only one or a little number of microbial species to supply a specific plant nutritional demand. In this study we tested the efficacy of the microbial consortium (MC) obtained from compost and the cyanobacteria Arthrospira platensis (AP) comparing with the application of the vermicompost tea (VT) and bokashi (BK) in arugula, lettuce, beetroot, and carrot in an agroforestry system in two seasons. Soil changes on chemical properties and β-glucosidase and arylsulfatase were measured over time. The vegetables yield was measured and for arugula and lettuce the nutritional traits and plant root system were also evaluated. Greater plant yield, nutritional values, and plant root development was observed in the CM treated plants, AP and BK had similar results. Our results show that both CM and AP have potential to become a sustainable product for agricultural production