The importance of sustainable use of natural resources, especially of soil and water, has been a subject of increasing relevance. The increase of human activity in ecosystems has great impact on the dynamics of soil organisms. The comparison between cultivated systems and native areas without anthropic interference can be used as soil quality index. Microorganisms are ideal indicators because they are very sensitive to changes and show variations in their community when subjected to stressful environments. The objective of the present study was to evaluate the quality of soil microbial abudance as an index of soil quality in agroecosystems Integrated Sustainable Agroecological Production, Agroforestry System and Isolation of springs in Brazilian Savanas. The experiment was conducted in the areas of the Vitória settlement, in the region of São Patrício Valley, Goianésia, Goiás, in an area of native "cerrado". The climate is classified as seasonal tropical (Aw), being characterized by two well defined seasons (dry and rainy), as well as with the occurrence of drought periods during the rainy season. The experimental design adopted was a 3 × 2 × 2 block factorial randomized with three replications, where factor 1 was represented by the systems used: Sustainable Integrated Agroecological Production (SIAP), Agroforestry System (AS) and springs isolation (SI), factor 2 was represented by the soil depth, 0-5 cm and 5-10 cm, and factor 3 was the installation time of the systems: 5 years and recently installed. Soil samples were collected at random in the rhizospheric soil in each plot. There was a greater number of fungal colonies in the AS system with 5 years of implantation, but did not differ with soil depth. There was a higher number of bacteria colonies in the SIAP system after 5 years. At the depth of 0 to 5 cm, the SIAP system had higher microbial abundance, but it was higher at 5 to 10 in AS system.