Lipid-based oleaginous microorganisms are potential candidates and resources for the sustainable production of biofuels. This study was designed to evaluate the performance of several alternative bio-based solvents for extracting lipids from yeasts. We used experimental design and simulation with Hansen solubility simulations and the conductor-like screening model for realistic solvation (COSMO-RS) to simulate the solubilization of lipids in each of these solvents. Lipid extracts were analyzed by high performance thin-layer chromatography (HPTLC) to obtain the distribution of lipids classes and gas chromatography coupled with a flame ionization detector (GC/FID) to obtain fatty acid profiles. Our aim was to correlate simulation with experimentation for extraction and solvation of lipids with bio-based solvents in order to make a preliminary evaluation for the replacement of hexane to extract lipids from microorganisms. Differences between theory and practice were noted for several solvents, such as CPME, MeTHF and ethyl acetate, which appeared to be good candidates to replace hexane.