The purpose of this work was to provide an integrated solution to the problem of optimising plant production flow while also optimising allergen control. That is, to improve process flows, improve equipment utilisation, reduce work-in-process (WIP) inventory, and reduce unnecessary movement of stock while also optimising allergen control in the area under investigation. Process improvement introduced to the plant during the project resulted in a 7% savings on labour cost, reduction in plant variability, reduced allergen cross contamination risk, reduced WIP, reduction of consumables, and increased equipment utilisation. Discrete event simulation software has been used to determine the preferred strategy for implementing allergen control in a food producing FMCG plant. Three preferred allergen control strategies were identified by the Company, which were then modelled and analysed for impact on labour cost. Furthermore, a study was done on the effect of plant layout on labour cost.