In the spirits industry, understanding the behaviour of volatile flavouring compounds (congeners) during distillation is important. This simulation study with the ProSim software®, BatchColumn, investigates the influence of different parameters of a multi-stage batch distillation on 57 congeners from five chemical families (alcohols, aldehydes, esters, acids, and terpenes). Industrial and laboratory scale whisky distillations were conducted with a fermented malted barley mash. The simulations illustrated the behaviour of volatile compounds based on how their volatility varied with ethanol concentration. The distribution of compounds between the different fractions (head, heart, tail and residue) was calculated. Further, optimisation strategies for the industrial distillation were tested by simulation. These included (1) cutting distillation later (ethanol mass fraction of 0.061 instead of 0.105) as the recovery of pleasant compounds is small compared to that of acids; (2) choosing an ethanol mass fraction during the heart extraction around 0.60 (67% v/v), rather than 0.67 (75% v/v) as it increases the recovery of compounds of interest and decreases the duration of distillation and energy costs and (3) enabling a higher concentration of ethanol at the beginning of the distillation to obtain better separation of aldehydes and esters.