Wastewater treatment system by activated sludge, the purification of the organic matter by specific heterogeneous microorganisms, occurs in the presence of oxygen in aeration tanks. The analysis of the microfauna present in the sludge is an important indicator of the performance and efficiency of the activated sludge system. Considering this importance, the objective of this work was to identify the microorganisms which are part of the microfauna present in the aeration tank of the effluent treatment plant of a soybean processing industry in the state of Mato Grosso, evaluating the biological activity of the sludge and the efficiency of the process. Protozoa and bacteria were identified through electronic microscopy and physical-chemical analyses such as pH, dissolved oxygen, nitrogen, phosphorus, BOD, COD, suspended solids, and SVI. During the study, it was possible to identify bacteria related to flake formation, organic matter degradation, nitrification and denitrification, and also microorganisms such as thecamoebas, micrometazoa, fixed ciliates and ciliates free natantes, characterizing the process with good purification and the structure of the sludge flakes between ideal and filamentous bulking with a high sludge age. The identification of the microfauna present was efficient as a bioindicator of the treatment system condition with removal of BOD and COD of 59.75 and 67.09%, respectively.