Methanol, a hepato- and neurotoxic compound, is present in apple-based beverages as a by-product of the enzymatic degradation of pectin. Stable isotope dilution assay (SIDA) employing gas chromatography-mass spectrometry (GC–MS) is the state-of-the-art method for methanol determination in beverages. Despite higher initial investment costs, quantitative 1H NMR spectroscopy (qNMR) is a simpler and faster analytical technique to quantify numerous analytes in liquid foods. Beyond targeted analyses, qNMR spectral fingerprints in the product might be used for non-targeted analytical goals, such as adulteration and contamination detections. Here, an existing 1H-qNMR method used for wine profiling was optimised for methanol quantification in apple-based products, including cross-validation against a SIDA-HS-GC–MS method and reference values from interlaboratory trials. The optimisation involved a pivotally important estimation of a correction factor by an external calibration approach, making qNMR results comparable to SIDA-HS-GC–MS. The optimised qNMR method is suggested to be an alternative for methanol quantification in beverages.