Liquefaction enzymes are often used during fermentation of fruit mashes to improve the yield of ethanol and the ability to pump the mash. The liquefaction enzymes hydrolyze pectin, but in addition to the desired pectin hydrolysis activity, the enzymes also have pectinesterase activity which hydrolyzes the methyl ester in pectin resulting in methanol formation. Fermentations of various apple varieties and Bartlett pears were conducted using liquefaction enzymes. The resulting distilled products contained concentrations of methanol above the legal limit of 280 mg/100 mL of 40% ethanol, with the observed methanol concentrations in a range between 320 and 656 mg/100 mL of 40% ethanol. In contrast to the undesired increase in methanol concentration, the enzymes provide only a marginal increase in ethanol yield. The results indicate that liquefaction enzymes should be used with caution for pomace fruit and that methanol monitoring should be implemented if these enzymes are used for commercial products.