The quantification of trace compounds in alcoholic beverages is a useful means to both investigate the chemical basis of beverage flavor and to facilitate quality control during the production process. One compound of interest is methanol which, due to it being toxic, must not exceed regulatory limits. The analysis of headspace gases is a desirable means to do this since it does not require direct sampling of the liquid material. One established means to conduct headspace analysis is selected ion flow tube mass spectrometry (SIFT-MS). The high concentration of ethanol present in the headspace of alcoholic drinks complicates the analysis, however, via reacting with the precursor ions central to this technique. We therefore investigated whether methanol could be quantified in the presence of a large excess of ethanol using SIFT-MS. We found that methanol reacted with ionized ethanol to generate product ions that could be used to quantify methanol concentrations and used this technique to quantify methanol in beverages containing different quantities of ethanol. We conclude that SIFT-MS can be used to quantify trace compounds in alcoholic beverages by determining the relevant reaction chemistry.