Fungal secondary metabolites comprise a wide range of bioactive and industrially relevant small molecules. The genes encoding the enzymes for the biosynthesis of such compounds are mostly organised in biosynthetic gene clusters (BGCs). Despite the insights that have been acquired so far, the transcriptional regulation of many BGCs remains enigmatic, thus impeding the valorisation of the respective secondary metabolites. The main cause is twofold, as 1) only a limited number of influencing factors has been investigated thoroughly and 2) only very few taxa have been studied, with a lack of studies in non-conventional yeasts in particular. However, some interesting and important biochemicals are produced by BGCs in such non-conventional yeasts. An example of the latter are sophorolipids (SLs), which are industrially relevant biochemicals (biosurfactants), produced by the non-conventional yeast Starmerella bombicola. The corresponding SL BGC will be investigated as a case study to gain more insight in the regulation of BGCs. To attain this objective, high-dimensional omics data will be generated related to regulation of SL biosynthesis, including the consideration of underexplored mechanisms. The acquired knowledge will positively impact the biosurfactant market and more generally the bio-economy.