Greenhouse gas emission during composting process is inevitable, although it relies on natural degradation. A good balance on carbon-to-nitrogen (C/N) ratio as well as the aeration mode could significantly control the emissions. The C/N ratio can be adjusted using optimal feedstock composition. The aeration can be done using passive and active modes. In the present study, greenhouse gas emissions during in-vessel co-composting of septage and organic waste with active and passive modes of aeration were investigated. This fills the gap in implementing suitable septage treatment practice. Retention of high temperature (> 55 °C) for prolonged period ensured the compost hygienization. The active aeration system showed significantly lower greenhouse gas emission compared to that of passive system. The contribution of CH4 and N2O to the total greenhouse gas was estimated to be 2.5% and 7.4% in the passive and 0.9% and 3.8% in the active aeration modes while > 90% was CO2. The resulted compost maturity was confirmed by seed germination index (> 80%) and NO3 −/NH4 + index (> 6.25). Our study highlight that in-vessel co-composting with active aeration is a suitable option to convert waste to a nutrient-rich fertilizer in a shorter period compared to other septage treatment options. © 2019, Islamic Azad University (IAU).