Methane clumped isotope signatures of abiogenesis may be diagnostic of the origin of methane on Earth and other planetary bodies. We performed synthesis of abiogenic methane in hydrothermal conditions between 130 and 300°C and determined δ13C, δD, Δ13CH3D, and Δ12CH2D2. The experiments were performed by heating water in the presence of Fe0 powder and CO. The reduction of water on metallic iron led to the formation of H2. CO was reacted with both H2 and H2O, generating both CH4 and CO2. Methane δ13C values are isotopically depleted by ∼25‰ relative to the CO starting material. This is consistent with carbon isotopic equilibrium between methane, carbon monoxide and carbon dioxide in our experiments. In contrast, D/H ratios are inconsistent with equilibrium isotopic fractionation, as illustrated by δD values of methane fractionated by ∼500‰ relative to starting H2O. This suggests that under our experimental conditions, hydrogen additions to carbon may be governed by kinetics. Δ13CH3D values track experimental temperature, with values between +1.5‰ and +5.0‰ for most samples. In contrast, Δ12CH2D2 values are displaced from equilibrium. We find exclusively negative Δ12CH2D2 values, showing deficits down to 40‰ relative to thermodynamic equilibrium. We interpret the data as evidence for distinct, kinetically induced D/H pools contributing to methane assembly, that is, a combinatorial effect. The cumulative D/H fractionations associated with CO hydrogenation explain the direction and magnitude of Δ12CH2D2 values during abiotic methane formation. We suggest that near equilibrium Δ13CH3D with negative Δ12CH2D2 signatures will help identify methane formed abiotically in nature.