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Organic agriculture is increasingly used as an alternative to conventional agriculture due to its positive impact on the health of ecosystems and agroecosystems. However, the outcome of organic agriculture in terms of the production of various crops remains uncertain due to the influence of many variables, rising questions about its advantages over conventional agriculture. This study assessed the impacts of organic agricultural systemon arbuscular mycorrhizal (AM) fungi diversity in soil and green tomato (Physalis ixocarpa Brot. ex Horn) crop production. A field experiment was conducted using a random block design with five repetitions of the following treatments: a) Control (no fertilization, NF); b) Vermicompost use (OTV); c) OTV with vermicompost leaching (OTH); and d) Inorganic fertilization (CST). Throughout the crop cycle, soil samples were analyzed chemically, the relative growth rate (RGR) of the plants was measured, and the colonization and diversity of AM fungi were quantified in roots and soil; finally, above-ground, root biomass, and fruit production were measured. Organic fertilization (OTV, OTH) increased (p < 0.05) RGR (10.47 cm OTV), AM colonization (21.80% on OTV and 20.95% on OTH) and diversity (21 species on OTV and 28 species on OTH), compared to CST treatment (8.18 cm on RGR; 15.17% AM colonization, and 11 species). Some AM species were uniquely associated with organic matter, phosphorous, cation exchange capacity and bulk density of soil on the organic system; however, biomass production and fruit yield did not differ (p > 0.05). It is concluded that organic agriculture management is essential to promote a greater AM fungi diversity and fungi root colonization. Plant-AM fungi interaction increasesgrowth rates and it allowsa similar tomato production compared with conventional agriculture. Inglés