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In situ and simultaneous measurement of the three most abundant isotopologues of methane using mid-infrared laser absorption spectroscopy is demonstrated. A field-deployable, autonomous platform is realized by coupling a compact quantum cascade laser absorption spectrometer (QCLAS) to a preconcentration unit, called trace gas extractor (TREX). This unit enhances CH₄ mole fractions by a factor of up to 500 above ambient levels and quantitatively separates interfering trace gases such as N₂O and CO₂. The analytical precision of the QCLAS isotope measurement on the preconcentrated (750 ppm, parts-per-million, µmole mole⁻¹) methane is 0.1 and 0.5 ‰ for <i>δ</i>¹³C- and <i>δ</i>D-CH₄ at 10 min averaging time. <br><br> Based on repeated measurements of compressed air during a 2-week intercomparison campaign, the repeatability of the TREX–QCLAS was determined to be 0.19 and 1.9 ‰ for <i>δ</i>¹³C and <i>δ</i>D-CH₄, respectively. In this intercomparison campaign the new in situ technique is compared to isotope-ratio mass spectrometry (IRMS) based on glass flask and bag sampling and real time CH₄ isotope analysis by two commercially available laser spectrometers. Both laser-based analyzers were limited to methane mole fraction and <i>δ</i>¹³C-CH₄ analysis, and only one of them, a cavity ring down spectrometer, was capable to deliver meaningful data for the isotopic composition. After correcting for scale offsets, the average difference between TREX–QCLAS data and bag/flask sampling–IRMS values are within the extended WMO compatibility goals of 0.2 and 5 ‰ for <i>δ</i>¹³C- and <i>δ</i>D-CH₄, respectively. This also displays the potential to improve the interlaboratory compatibility based on the analysis of a reference air sample with accurately determined isotopic composition.