Preconcentration of methane (CH4) from air is a critical sampling step in the measurement of singly and doubly substituted isotopologue ratios. We demonstrate the potential for isotope fractionation during preconcentration onto and elution from the common trapping material HayeSep-D and investigate its significance in laser spectroscopy measurements. By altering the trapping temperature for adsorption, the flow direction of CH4 through the trap and the time at which CH4 is eluted during a desorption temperature ramp, we explain the mechanisms behind fractionation affecting δ13C(CH4) and δ2H(CH4). The results highlight that carbon isotope fractionation is driven by advection and diffusion, while hydrogen isotope fractionation is driven by the interaction of CH4 with the adsorbing material (tending to smaller isotopic effects at higher temperatures). We have compared the difference between the measured isotope ratio of sample gases (compressed whole air and a synthetic mixture of CH4 at ambient amount fraction in an N2 matrix) and their known isotopic composition. An open-system Rayleigh model is used to quantify the magnitude of isotopic fractionation affecting measured δ13C(CH4) and δ2H(CH4), which can be used to calculate the possible magnitude of isotopic fractionation given the recovery percentage. These results provide a quantitative understanding of isotopic fractionation during the sample preparation of CH4 from ambient air. The results also provide valuable insights applicable to other cryogenic preconcentration systems, such as those for measurements that probe the distribution of rarer isotopologues.