© Author(s) 2019. Emission estimates of carbon dioxide (CO2) and methane (CH4) and the meteorological factors affecting them are investigated over Sacramento, California, using an aircraft equipped with a cavity ring-down greenhouse gas sensor as part of the Alpha Jet Atmospheric eXperiment (AJAX) project. To better constrain the emission fluxes, we designed flights in a cylindrical pattern and computed the emission fluxes from two flights using a kriging method and Gauss's divergence theorem. Differences in wind treatment and assumptions about background concentrations affect the emission estimates by a factor of 1.5 to 7. The uncertainty is also impacted by meteorological conditions and distance from the emission sources. The vertical layer averaging affects the flux estimate, but the choice of raw wind or mass-balanced wind is more important than the thickness of the vertical averaging for mass-balanced wind for both urban and local scales. The importance of vertical mass transfer for flux estimates is examined, and the difference in the total emission estimate with and without vertical mass transfer is found to be small, especially at the local scale. The total flux estimates accounting for the entire circumference are larger than those based solely on measurements made in the downwind region. This indicates that a closed-shape flight profile can better contain total emissions relative to a one-sided curtain flight because most cities have more than one point source and wind direction can change with time and altitude. To reduce the uncertainty of the emission estimate, it is important that the sampling strategy account not only for known source locations but also possible unidentified sources around the city. Our results highlight that aircraft-based measurements using a closed-shape flight pattern are an efficient and useful strategy for identifying emission sources and estimating local- and city-scale greenhouse gas emission fluxes.