A method based on headspace-isotope dilution (HS-ID) GC-MS for the quantitative analysis of methoxyl and ethoxyl groups in any kind of lignin has been developed. The method involves the application of an isotopically labeled internal standard (4-(methoxy-d₃)-benzoic acid and 4-(ethoxy-d₅)-benzoic acid), which, together with lignin, undergoes standard hydroiodic acid cleavage of methoxyl and ethoxyl groups, followed by headspace GC-MS analysis of the respective deuterated and non-deuterated iodomethanes and iodoethanes. As also the internal standard is generated in situ during ether cleavage, any variations in the procedure are levelled out. The application of the isotopically labeled internal standard essentially increased the robustness of the overall approach. The accuracy and precision of methoxyl and ethoxyl group quantification in lignins have been assessed, and the data were compared to the classical Zeisel–Vieböck–Schwappach method for methoxyl groups in lignins. The novel approach for methoxyl and ethoxyl group determination showed a more satisfactory precision, accuracy, and also a much higher sample throughput, with approximately 40 samples per day.