The purpose of this dissertation was to assess the practicality of using microbial fuel cells (MFCs) as alternative sanitation systems for wastewater treatment and energy recovery, focusing on identifying key design considerations for treating high strength wastewater and managing alternative metabolic pathways. We evaluated the energetic outputs of a lab-based pilot MFC designed to treat complex organics present in both synthetic feces and municipal wastewater. The pilot MFC produced two energetic products, methane and electricity, when treating two types of complex wastewaters. The energetic products associated with anode respiration and methanogenesis were simultaneously observed and yielded a combined energy ouput of 3.3 ± 0.64 W/m3 when treating synthetic feces wastewater and 0.40 ± 0.07 W/m3 when treating municipal wastewater. We also evaluated the impacts of electrolytes (primarily as conductivity and pH) on the electrochemical peformance of MFCs using augmented inoculums. Under electrolytically-stressed anode environments, augmenting the inocula (primary wastewater) with microorganisms from acidic and high-salts environments improve the electrochemical performance of a MFC under high conductivities (5.2-37 mS/cm) and low pH (4.1-6.2). The final section is focused on the role of external resistances, or external load, and its impact on electrochemical performance in MFCs when methanogenesis inhibitors are present in the anode. Our study observed that external resistance had a significant influence on the anode potential and power and current densities. When MFCs are operated at low external resistances (17 and 170 W), the addition of 2-BES caused anode potential to decrease to values between -0.1 and 0 mV vs SHE. An increase in current density and CE during these periods suggest that shifts to lower anode potentials triggered c-type cytochromes that are only active within that specific range of redox pontential. During periods when nitrate was present in the anode, CE and current densities decreased at all external resistances except at 1800 W. Although higher power and current densities were observed at low external resistances, they were not sustained throughout the experimental period. Consistent current output was more readily observed at high external resistances (820 and 1800 W), demonstrating the electrochemical robustness of the biofilms exposed to pertubations of the anode environment at more negative anode potentials.