Sustainable production in an agro-ecosystem derives from the balance between plants, soils and organisms. The objective of this work was to evaluate the rate of mycorrhizal colonization and spore density as an index of soil quality in agricultural ecosystems in the region of Vale do São Patrício. The experiment was conducted in the areas of settlements, new dawn and Itajá in Goianésia-Goiás. The experimental design was a factorial 5 x 3 in randomized blocks with three replications plus the additional comparative treatment of native Cerrado (vegetation typical of the Brazilian interior), where the factor 1 was represented by systems used: Ecological Sustainable Integrated Production, Agrossilvipastoril System, Agroforestry System and Isolation of springs. Factor 2 was represented by the time of installation of systems: 4 years, 2 years, and newly installed. There were no differences between the treatments studied. Independent of the agroecosystem and the age of systems, the density of spores and the rate of colonization were equivalent to the system of native Cerrado.