Single-cell oil (SCO) produced in biorefineries from oleaginous yeasts is an emerging sustainable alternative to mineral and plant-based oils. The unconventional yeast Cutaneotrichosporon oleaginosus has particularly drawn attention for its high SCO yields. In addition, C. oleaginosus can serve as a microbial cell factory for such value-added co-products. In the first part of this work, the potential of squalene production with C. oleaginosus – a high-value compound for the food, pharmaceutical and cosmetic industries – was investigated. The second part of this work focuses on tools for genetic modification of C. oleaginosus. This will expand the options for high-value oleochemical production in this yeast. Concluding, this work contributes to further establishing oleaginous yeast biorefineries as a cost-efficient, flexible platform to produce sustainable oils and oil-based products.