The oleaginous yeast Yarrowia lipolytica is capable of accumulating large amounts of fatty acids in the form of lipids which can serve as a platform polymer for a variety of applications. Additionally, through heterologous gene expression, Y. lipolytica is capable of producing carotenoids. Due to the observation that Y. lipolytica exhibits a high phenotypic inter-strain variability, robotics and microwell scale cultivations are applied to examine 12 wild type strains of a Y. lipolytica collection. The strains are characterized with respect to their metabolic capabilities for fatty acid production as well as genetically manipulated to produce beta-carotene. Furthermore, growth and production behavior of the strain collection at different temperatures as well as initial pH are assessed. A molecular discrimination between the strains is achieved by internal transcribed spacer (ITS)-sequencing and polymerase chain reaction (PCR)-based methods. The best performing strain with respect to lipid production produces ≈2% lipids per dry cell weight (DCW) and 8 mg g −1 beta-carotenoids in yeast nitrogen base (YNB) media. All strains show robust growth from 28 to 34°C. Practical Applications: Unlocking nature's potential by screening natural isolates shows that even on inter-strain level sufficient phenotypic diversity may arise. Automated growth-based characterization of beta-caroteneproducing strains in terms of media composition, effect of initial pH, and temperature tolerance shows that with modern cultivation techniques, rapid characterization of strain collections is feasible. Combining results of beta-carotene and lipid formation could help to balance both pathways to improve the storage of hydrophobic compounds in the lipid droplets. The generalized findings could be further transferred to improve the production of any valuable compound, derived from the mevalonate pathway.