Craft breweries release wastewater into the environment, posing serious environmental concerns. Microbial fuel cells (MFCs) are an attractive technology that has been used in industrial wastewater treatment. This study used a scalable system of nine MFCs (stacked) to treat 150 L of craft brewery wastewater (CBW). The CBW had 1831 ± 85 mg COD (chemical oxygen demand) L−1. The hydraulic retention time was 5 days, with a COD removal percentage of 93 ± 1.8%. The total internal resistance of the stack was 204.8 ± 5.2 Ω at 26 ± 2 °C without the use of a metal catalyst; the reduction of oxygen was the limiting process. Finally, the sequence of treatments applied with this proposed system demonstrated its self-sustainability, which could be a viable option for the real-life conditions of this kind of wastewater. Further research is needed.