The volatile fraction of natural products often consists of complex mixtures of isomeric and/or homologous components with similar structural and physical characteristics (e.g. mono- and sesquiterpenoids) that are not easy to separate simultaneously with conventional GC stationary phases, even when used with multidimensional systems. The introduction of ionic liquids (ILs) as stationary phases has opened up new perspectives in this field as their unique solvation properties result in uncommon selectivity, which is completely different to that of classic polydimethylsiloxane (PDMS)- and polyethyleneglycol (PEG)-based columns. Because of their peculiar selectivity and high inertness, IL-based columns have already found several applications in the natural product field in mono- and multidimensional GC and preparative GC, leading to the exhaustive analysis of complex samples (including aqueous solutions), and the separation of challenging pair(s) of compounds. This article provides an overview of how IL-based columns can be exploited in the fields of food and natural products, explores the wide range of applications that have already been developed and highlights the main features of these promising stationary phases, which are expected to be further extended in the near future, in particular, for routine use.