Quantifying and understanding methane emissions of cities are of great importance given their role in current and future mitigation efforts to combat climate changing emissions. However, it remains challenging to routinely and accurately characterize and verify city-scale methane emission inventories. Previous studies of urban methane emissions have employed a range of emission quantification methods, leading to inconsistent estimates and different associated uncertainties. As a result, a robust and widely applicable framework for quantifying urban emissions remains lacking. In this study, we describe our development of an advanced mass balance emissions accounting  using TROPOspheric Monitoring Instrument (TROPOMI) satellite observations to estimate the orbit-level net bulk (city-level) methane emissions and corresponding emissions uncertainties due to the method. We have tested and demonstrated that the novel integration of hourly-resolved wind data under the planetary boundary layer (PBL) enables a more conceptually-accurate assessment of methane emissions from urban areas than methods that do not consider thermodynamic variability. In addition, we have introduced an upwind-based approach for background determination, in which background methane concentrations were defined using city-adjacent regions along the PBL-pressure-weighted-mean upwind direction. Initial assessments with this approach were tested for three megacities (London, Los Angeles and New York) between 2021 and 2023. Results indicate that existing emission inventories generally underestimate urban methane emissions across all three cities, but with significant inter-annual and inter-city variability. Satellite-derived emissions from 2021 to 2023 range from 5.99 to 11.90 t h^-1 in London, 26.21 to 62.77 t h^-1 in Los Angeles, and 30.85 to 44.77 t h^-1 in New York, corresponding to factors of approximately 0.1–2.0, 0.3–2.1, and 5.1–9.2 times the inventory estimates, respectively. Compared with previous top-down urban studies for the same cities, our emission estimates are generally lower but remain broadly consistent when differences in urban extent are taken into account. These results demonstrate that satellite observations can facilitate ongoing city-scale emission quantification, support inventory reconciliation and reporting, offer the potential for long-term monitoring globally, and further aid efforts to assess whether stated methane emission targets are being met.