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Soil microorganisms play an important role on plant development and the homogenization of soil microbiomes is harmful to agri-environments. It is essential that agricultural practices are carried out by taking soil microbiome preservation in consideration. Agroforestry systems are one of the most environmentally friendly agrosystems and its plant diversity directly influences the soil microbiome diversity. In this study, we tested the efficacy of the microbial consortium (MC) obtained from compost and the cyanobacteria Arthrospira platensis (Ap) compared with the application of the vermicompost tea (VT) and bokashi (Bk) in arugula, lettuce, beetroot, and carrot in two seasons in a recently implemented agroforestry system. We aimed to verify if MC and Ap could be new promising sustainable alternatives in vegetables production. The strategy can be broken down into three stages: (1) Green manure management: planting, cutting, griding, and incorporation in the soil, (2) agroforestry system implementation, and (3) treatment application in a completely randomized blocks design. The vegetables yield was measured. Nutritional traits and the plant root system were evaluated for arugula and lettuce. Greater plant yield, nutritional values, and plant root development were observed in the MC-treated plants; Ap and Bk had, in general, similar results. Our data show that both MC and Ap have potential to become a sustainable product for agricultural production. [ABSTRACT FROM AUTHOR]