Natural gas transmissions and storage compressor stations account for the largest share of methane (CH4) emissions in New York State (NYS). Yet, NYS’s CH4 emissions inventory is based on measurements that are a decade old and unlikely to be representative of NYS operations. Here, we present results from a comprehensive, multi-scale aerial CH4 measurement campaign across all NYS transmission and storage compressor stations. We find a skewed emissions distribution, with 20% of stations accounting for 74% of total CH4 emissions. Emissions at engine-driven compressor stations are, on average, 3-4x higher than emissions at turbine-driven compressor stations, thus demonstrating the need for separate emissions factors for engine- and turbine-drive compressor stations. Overall, measurement-informed emissions inventory from midstream transmission and storage compressor stations in NYS are 72% and 69% lower than the current NYS inventory, respectively. We estimate updated emissions factors of 464 [95% CI: 162 – 920] metric ton (MT) CH4/station/yr and 139 [97, 191] MT CH4/station/yr for engine- and turbine-based transmission compressor stations, respectively. Similarly, we estimate an updated emissions factor of 413 [164, 733] MT CH4/station/yr for engine-based storage compressor stations. These updated emissions factors, along with improved activity data, enable effective reconciliation of NYS inventory with measured emissions.