RationaleMeasurement of greenhouse gas (GHG) concentrations and isotopic compositions in the atmosphere is a valuable tool for predicting their sources and sinks, and ultimately how they affect Earth's climate. Easy access to unmanned aerial vehicles (UAVs) has opened up new opportunities for remote gas sampling and provides logistical and economic opportunities to improve GHG measurements.MethodsThis study presents synchronized gas chromatography/isotope ratio mass spectrometry (GC/IRMS) methods for the analysis of atmospheric gas samples (20‐mL glass vessels) to determine the stable isotope ratios and concentrations of CO2, CH4 and N2O. To our knowledge there is no comprehensive GC/IRMS setup for successive measurement of CO2, CH4 and N2O analysis meshed with a UAV‐based sampling system. The systems were built using off‐the‐shelf instruments augmented with minor modifications.ResultsThe precision of working gas standards achieved for δ13C and δ18O values of CO2 was 0.2‰ and 0.3‰, respectively. The mid‐term precision for δ13C and δ15N values of CH4 and N2O working gas standards was 0.4‰ and 0.3‰, respectively. Injection quantities of working gas standards indicated a relative standard deviation of 1%, 5% and 5% for CO2, CH4 and N2O, respectively. Measurements of atmospheric air samples demonstrated a standard deviation of 0.3‰ and 0.4‰ for the δ13C and δ18O values, respectively, of CO2, 0.5‰ for the δ13C value of CH4 and 0.3‰ for the δ15N value of N2O.ConclusionsResults from internal calibration and field sample analysis, as well as comparisons with similar measurement techniques, suggest that the method is applicable for the stable isotope analysis of these three important GHGs. In contrast to previously reported findings, the presented method enables successive analysis of all three GHGs from a single ambient atmospheric gas sample.