This study treated sanitary landfill leachate and was conducted in a pilot-scale system composed of three serial ponds (P1, P2 and P3), followed by a rock filter, in order to evaluate the microbial consortium influence on system performance and to investigate microorganism dynamics in the process. The system was broken into three stages, with a continuous flow rate (Q = 200 L d−1) for 43 weeks. The stages were as follows: conventional operation (stage I), 12 h aeration in P2 (stage II), and 18 h aeration in P2 (stage III). The results showed the possibilities for treating landfill leachate, presenting an average efficiency of 75% for both filtered biochemical oxygen demand and ammonium. At the end of stage III, the ammonium concentration was 6 mg L−1, which is lower than that established by Brazilian regulations for wastewater discharge (CONAMA 430/2011). The aeration applied in P2 led to a change in the microbial consortia during the second and third stage, which influenced the quality of the final effluent. The best performance was seen in stage III, where the system showed high microbial diversity, including the presence of nitrifying bacteria.