This study characterised the behaviour of congeners during the multi-stage discontinuous distillation of whisky using a Stupfler-type still. It also investigated the influence of recycling the head and tail fractions on the composition of the unaged spirit and, for the compounds with known equilibrium data, to validate the capability of software tools to simulate their behaviour during distillation. To this end, profile curves of ethanol (% ABV) and 45 aroma compounds (mg/L) during distillation are reported with 27 compounds, compared to simulated data using ProSim® BatchColumn software. Further, the mass distribution of each compound between the fractions of discarded head, recycled head, heart, tail and residue are estimated. Assuming that this distribution was maintained during each distillation, it was shown that for the wash, a pseudo-steady state was achieved in less than five distillations, and the true recovery rate of each compound in the heart was assessed. This study clearly demonstrates that during distillation, the congeners behave according to the ethanol content of the boiling liquid in the column. It provides real information on the separation of volatile compounds with a batch still with a distillation column above the heater. Additionally, the data highlights the importance to the unaged spirit of recycling the head and tail fractions. These results provide useful information for distillers to choose the appropriate way of collecting the heart fraction.