The Coronavirus Disease-2019 (COVID-19) outbreak is an unprecedented global pandemic, sparking grave public health emergencies. One of the measures to reduce COVID-19 transmissions recommended by the World Health Organization is hand hygiene, i.e., washing hands with soap and water or disinfecting them using an alcohol-based hand sanitiser (ABHS). Unfortunately, competing ABHSs with unknown quality, safety, and efficacy thrived, posing yet another risk to consumers. This study aims to develop, optimise, and validate a gas chromatography-mass spectrometry (GC–MS)-based analytical method to simultaneously identify and quantify ethanol or isopropyl alcohol as the active ingredient in ABHS, with simultaneous determination of methanol as an impurity. The GC–MS was operated in Electron Ionisation mode, and Selected Ion Monitoring was chosen as the data acquisition method for quantitation. The analytical method was validated for liquid and gel ABHSs, covering the specificity, linearity and range, accuracy, and precisions, including the limit of detection and the limit of quantitation. The specificity of each target analyte was established using the optimised chromatographic separation with unique quantifier and qualifier ions. The linearity was ascertained with a coefficient of determination (r2) of > 0.9994 over the corresponding specification range. Respectively, the accuracy and precisions were satisfactory within 98.99 to 101.09% and < 3.04% of the relative standard deviation. The method was successfully applied to 69 ABHS samples, where 14 contained insufficient amounts of the active ingredient. Alarmingly, four samples comprised a high amount of methanol ranging from 5.3 to 19.4% with respect to the active alcohol percentage, which may pose significant short- and long-term health issues, leading to life-threatening crises for consumers. The method established would benefit in protecting the public against the potential harm due to substandard or unsafe ABHS products, primarily due to the presence of hazardous impurities such as methanol.