Lignin is a major structural plant biochemical and biogeochemical compound present in peat and lignite. Its monomeric (phenolic) and polymeric structures include varying amounts of ether-bonded methyl groups (i.e., methoxy or OCH3). These methoxy groups are generally underused targets for both structural characterization and isotopic analyses. We analyzed the quantity and C and H isotopic composition of methoxy groups within a range of substrates including lignin phenols, lignin, wood, peat, lignite, and sub-bituminous and bituminous coal. We used the Zeisel method to cleave the ether bonds with hydroiodic acid to yield iodomethane which can be analyzed by gas chromatography (GC). Finding inconsistent transfer and isotope effects associated with room temperature headspace injections, we instead used isooctane as a solvent for the iodomethane analyte (the liquid method). Using the liquid method, we obtained a linear response by GC-flame ionization detection (GC-FID) for iodomethane and a linear calibration and 85 ± 6% recovery of methyl from methoxy groups from solid standards of phenolic compounds of known stoichiometry. We introduced quantification via lignin phenolic compounds to calibrate both analytical and experimental yield. Methyl yields provided structural information and confirmed that lignin oxidation products (LOPs) from copper oxide oxidation underestimate the number of methoxy-bearing phenols (yield < 0.3 of expected based on stoichiometry); in combination the two approaches provide structural information and quantification. We found that concentrations of methyl from methoxy groups in geologic sediments (lignite, sub-bituminous and bituminous coal) initially increase with diagenesis as lignin to cellulose ratio increases, and then decline to low concentrations during coalification, offering new possibilities for characterizing the transformation of peat and lignite. We assessed an array of plant biochemicals and established that natural and synthetic methoxy groups span a broad range of dual stable carbon and hydrogen isotopic compositions indicating scope for biogeochemical and forensic applications.