Airborne measurements within the urban mixing layer (360 m) over Greater London are used to quantify CO2 emissions at the meso-scale. Daytime CO2 fluxes, calculated by the Integrative Mass Boundary Layer (IMBL) method, ranged from 46 to 104 μmol CO2m−2s−1 for four days in October 2011. The day-to-day variability of IMBL fluxes is at the same order of magnitude as for surface eddy-covariance fluxes observed in central London. Compared to fluxes derived from emissions inventory, the IMBL method gives both lower (by −37%) and higher (by 19%) estimates. The sources of uncertainty of applying the IMBL method in urban areas are discussed and guidance for future studies is given. •CO2 was measured by aircraft in London within the urban mixing layer (360 m).•Meso-scale urban emissions were estimated using aircraft observations.•Airborne-fluxes within −37% and 20% of emissions from inventory.•Airborne-fluxes within the range of eddy-covariance observations in central London. CO2 airborne-derived fluxes by Boundary Layer Mass balance are an independent measure of meso-scale urban fluxes complementing urban eddy-covariance fluxes and emissions inventory.