Advanced onsite wastewater treatment systems (OWTS) designed to remove nitrogen from residential wastewater play an important role in protecting environmental and public health. Nevertheless, the microbial processes involved in treatment produce greenhouse gases (GHGs) that contribute to global climate change, including CO2, CH4, N2O. We measured GHG emissions from 27 advanced N-removal OWTS in the towns of Jamestown and Charlestown, Rhode Island, USA, and assessed differences in flux based on OWTS technology, home occupancy (year-round vs. seasonal), and zone within the system (oxic vs. anoxic/hypoxic). We also investigated the relationship between flux and wastewater properties. Flux values for CO2, CH4, and N2O ranged from -0.44 to 61.8, -0.0029 to 25.3, and -0.02 to 0.23 µmol GHG m-2 s-1, respectively. CO2 and N2O flux varied among technologies, whereas occupancy pattern did not significantly impact any GHG fluxes. CO2 and CH4 - but not N2O - flux was significantly higher in the anoxic/hypoxic zone than in the oxic zone. Greenhouse gas fluxes in the oxic zone were not related to any wastewater properties. CO2 and CH4 flux from the anoxic/hypoxic zone peaked at ~22-23 °C, and was negatively correlated with dissolved oxygen levels, the latter suggesting that CO2 and CH4 flux result primarily from anaerobic respiration. Ammonium concentration and CH4 flux were positively correlated, likely due to inhibition of CH4 oxidation by NH4+. N2O flux in the anoxic/hypoxic zone was not correlated to any wastewater property. We estimate that advanced N-removal OWTS contribute 262 g CO2 equivalents capita-1 day-1, slightly lower than emissions from conventional OWTS. Our results suggest that technology influences CO2 and N2O flux and zone influences CO2 and CH4 flux, while occupancy pattern does not appear to impact GHG flux. Manipulating wastewater properties, such as temperature and dissolved oxygen, may help mitigate GHG emissions from these systems.