This study monitored the start-up and operation of an activated sludge system at a poultry and fish slaughterhouse located in western Paran & aacute; state, Brazil. The physicochemical parameters pH, chemical oxygen demand, biochemical oxygen demand, total suspended solids, volatile suspended solids, fixed suspended solids, total nitrogen, ammoniacal nitrogen, and phosphorus were determined in different stages of the system: anoxic pond, biological reactor, and secondary settler. Based on these results, calculations were made regarding the parameters used in operational control: sludge volume index, volumetric organic load, food/microorganism ratio, sludge age and sludge discharge. Microscopy analyses of the biological sludge enabled assessment of the predominant microfauna during the development of the treatment. With stabilization of the microfauna inside the biological reactor, four months after the start of operation, there were improvements in removal efficiencies with average values for chemical oxygen demand, biochemical oxygen demand, total nitrogen and ammonia nitrogen of 84, 88, 46 and 81%, with maximum efficiencies of 97, 99, 71 and 99%, respectively. Phosphorus removal was not satisfactory, which could be attributed to the high age of the sludge (> 40 days) and the pH range maintained during the treatment (6.0-6.5). The microscopy analyses of the biological sludge revealed a variety of microorganisms, with the species predominance depending on the treatment stage. Initially, there was the presence of fixed amoebas, flagellates, and ciliates. With improvement of biological floc formation, there was the appearance of rotifers, Thecamoeba, and floc predator ciliates, which are essential microorganisms for the excellent performance of the system.