We present the first sector-specific analysis of methane (CH4) emissions from the San Francisco Bay Area (SFBA) using CH4 and volatile organic compound (VOC) measurements from six sites during September – December 2015. We apply a hierarchical Bayesian inversion to separate the biological from fossil-fuel (natural gas and petroleum) sources using the measurements of CH4 and selected VOCs, a source-specific 1 km CH4 emission model, and an atmospheric transport model. We estimate that SFBA CH4 emissions are 166–289 Gg CH4/yr (at 95% confidence), 1.3–2.3 times higher than a recent inventory with much of the underestimation from landfill. Including the VOCs, 82 ± 27% of total posterior median CH4 emissions are biological and 17 ± 3% fossil fuel, where landfill and natural gas dominate the biological and fossil-fuel CH4 of prior emissions, respectively.