Electrochemical systems are an attractive option for onsite latrine wastewater treatment due to their high efficiency and small footprint. While concerns remain over formation of toxic byproducts during treatment, rigorous studies examining byproduct formation are lacking. Experiments treating authentic latrine wastewater over variable treatment times, current densities, chloride concentrations, and anode materials were conducted to characterize byproducts and identify conditions that minimize their formation. Production of inorganic byproducts (chlorate and perchlorate) and indicator organic byproducts (haloacetic acids and trihalomethanes) during electrolysis dramatically exceeded recommendations for drinking water after one treatment cycle (∼10-30 000 times), raising concerns for contamination of downstream water supplies. Stopping the reaction after ammonium was removed (i.e., the chlorination breakpoint) was a promising method to minimize byproduct formation without compromising disinfection and nutrient removal. Though treatment was accelerated at increased chloride concentrations and current densities, byproduct concentrations remained similar near the breakpoint. On TiO2/IrO2 anodes, haloacetic acids (up to ∼50 μM) and chlorate (up to ∼2 μM) were of most concern. Although boron-doped diamond anodes mineralized haloacetic acids after formation, high production rates of chlorate and perchlorate (up to ∼4 and 25 μM) made them inferior to TiO2/IrO2 anodes in terms of toxic byproduct formation. Organic byproduct formation was similar during chemical chlorination and electrolysis of wastewater, suggesting that organic byproducts are formed by similar pathways in both cases (i.e., reactions with chloramines and free chlorine).