Biogas purification via water scrubbing produces effluent containing dissolved CH4, H2S, and CO2, which should be removed to reduce greenhouse gas emissions and increase its potential for water regeneration. In this study, a reactor built with air supplies at the top and bottom was utilized for the treatment of biogas purification effluent through biological oxidation and physical stripping processes. Up to 98% of CH4 was removed through biological treatment at a hydraulic retention time of 2 hr and an upper airflow rate of 2.02 L/day. Additionally, a minimum CH4 concentration of 0.04% with no trace of H2S gas was detected in the off gas. Meanwhile, a white precipitate was captured on the carrier showing the formation of sulfur. According to the developed mathematical model, an upper airflow rate of greater than 2.02 L/day showed a small deterioration in CH4 removal performance after reaching the maximum value, whereas a 50 L/day bottom airflow rate was required to strip the CO2 efficiently and raise the effluent pH from 5.64 to 7.3. Microbiological analysis confirmed the presence of type 1 methanotroph communities dominated by Methylobacter and Methylocaldum. However, bacterial communities promoting sulfide oxidation were dominated by Hyphomicrobium.