Understanding the chemical composition of whisky and the impact of each step in the manufacturing process provides a basis for responding to the challenges of producing high quality spirits. In this study, the objective was to discriminate whiskies according to their geographical origin and authenticate the maturation time in cask based on the non-volatile profiles. The combination of FT-ICR-MS and chemometrics allowed the distinction of whiskies from four geographical origins in Scotland (Highlands, Lowlands, Speyside and Islay). Statistical modeling was also used to discriminate whiskies according to the maturation time in cask and reveal chemical markers associated with the ageing regardless of the origin or the production process. Interestingly, the flow of transfer of compounds from wood barrels to distillates is not constant and homogeneous over the maturation time. The largest transfer of compounds from the barrel to the whisky was observed around twelve years of maturation.