The intensive measurement campaign CoMet 1.0 (Carbon Dioxide and Methane Mission) took place during May and June 2018, with a focus on greenhouse gases over Europe. CoMet 1.0 aimed at characterising the distribution of CH4 and CO2 over significant regional sources with the use of a fleet of research aircraft as well as validating remote sensing measurements from state-of-the-art instrumentation installed on board against a set of independent in situ observations. Here we present the results of over 55 h of accurate and precise in situ measurements of CO2, CH4 and CO mole fractions made during CoMet 1.0 flights with a cavity ring-down spectrometer aboard the German research aircraft HALO (High Altitude and LOng Range Research Aircraft), together with results from analyses of 96 discrete air samples collected aboard the same platform. A careful in-flight calibration strategy together with post-flight quality assessment made it possible to determine both the single-measurement precision as well as biases against respective World Meteorological Organization (WMO) scales. We compare the result of greenhouse gas observations against two of the available global modelling systems, namely Jena CarboScope and CAMS (Copernicus Atmosphere Monitoring Service). We find overall good agreement between the global models and the observed mole fractions in the free tropospheric range, characterised by very low bias values for the CAMS CH4 and the CarboScope CO2 products, with a mean free tropospheric offset of 0 (14) nmol mol−1 and 0.8 (1.3) µmol mol−1 respectively, with the numbers in parentheses giving the standard uncertainty in the final digits for the numerical value. Higher bias is observed for CAMS CO2 (equal to 3.7 (1.5) µmol mol−1), and for CO the model–observation mismatch is variable with height (with offset equal to −1.0 (8.8) nmol mol−1). We also present laboratory analyses of air samples collected throughout the flights, which include information on the isotopic composition of CH4, and we demonstrate the potential of simultaneously measuring δ13C−CH4 and δ2H−CH4 from air to determine the sources of enhanced methane signals using even a limited number of discrete samples. Using flasks collected during two flights over the Upper Silesian Coal Basin (USCB, southern Poland), one of the strongest methane-emitting regions in the European Union, we were able to use the Miller–Tans approach to derive the isotopic signature of the measured source, with values of δ2H equal to −224.7 (6.6) ‰ and δ13C to −50.9 (1.1) ‰, giving significantly lower δ2H values compared to previous studies in the area.