The yield of soybean was influenced by the chemical and microbiological properties of the soil, which was favored by management techniques that promote improvement in soil quality. The objective of this study was to evaluate soybean yield, chemical and microbiological quality of the soil as a function of biological fertilization and soil cover conditions. The experiment was conducted in both crops seasons 2015/16 and 2016/17 with experimental design in randomized blocks, with the agronomic characteristics of the soybean analyzed as a function of the factors of biological fertilization and soil cover conditions, as well as the chemical and microbiological indicators of the soil, besides the two factors mentioned earlier, fragment of forest. It was observed higher height of plants, pods with three grains, leaf area and yield of soybean cultivated on Crotalaria ochroleuca, followed by Pennisetum glaucum. Biological fertilizer, P. glaucum and C. ochroleuca promoted increases in the fertility of soil cultivated with soybean, mainly potassium, and contributed to reduce carbon losses, indicated by lower basal respiration and soil metabolic quotient. Based on the results, we conclude that the soybean presented highest grain yield with C. ochroleuca, and the biological fertilization and cover plants increased the chemical and microbiological quality of the soil. These techniques can be implemented in the soybean farming system.