Developing countries are confronted with general issues of municipal wastewater management and treatment. Untreated wastewater and faecal sludge from septic tanks and traditional toilets are often discharged into rivers and used for urban agriculture without any treatment to minimize potential biorisks. Such practices result in potential environmental and public health risks. In this study, a wastewater treatment plant prototype coupled with Moringa oleifera seeds treatment was developed to evaluate their effectiveness for the reduction of faecal indicator bacteria and antibiotic-resistant bacteria in domestic wastewater. We demonstrated that that the proposed wastewater treatment plant prototype reduces bacteria by 99.34%. A high removal of the bacteria load was obtained after the addition of Moringa oleifera seeds into waters, with removal rates of 36.6–78.8% for E. coli, 28.3–84.6% for faecal coliform, 35.3–95.6% for Vibrio cholera and 32.1–92.4% for total flora. A similar effect of Moringa oleifera seeds was noted for the removal of antibiotic-resistant bacteria, extended-spectrum beta-lactamases and carbapenem-resistant Enterobacteriaceae, with a removal rate of up to 98% for E. coli and faecal coliform, 100% for Vibrio cholera and 91.96% for total flora. This study demonstrated the high removal efficiency pathogens and antibiotic-resistant bacteria from domestic wastewater using Moringa oleifera seeds.