The use of microorganisms to produce aroma molecules is growing in the flavor and fragrance industries due to the increased market for natural products. In this study, the effect of the type of microorganism, and cellular permeabilization on the production of aroma molecules from castor oil by liquid fermentation with yeasts, was assessed for possible application in the production of natural flavors. Different treatments were assessed with a three-way factorial design (type of microorganism, cell permeabilization and amount of castor oil), the aroma profile was analyzed using gas chromatography with mass spectrometry (GC-MS), and the treatments were classified by principal component analysis (PCA). The results showed a significant effect of the yeast S. cerevisiae and Z. rouxii , the permeabilization treatment, and the amount of castor oil in the production of aroma compounds (p < 0.05). The molecules 4-hydroxy-2-pentenoic acid γ-lactone, methyl pyruvate, 2,3,4-trimethyl-3-pentanol, and δ-decalactone were affected by all the factors. The production of metabolites increased with the permeabilization treatments for certain molecules like ethanol and organic acids, whereas the generation of others decreased. The use of these microorganisms and cell permeabilization are promising approaches for producing molecules with applications in natural flavors. • Fermentation of castor oil produce different aromatic compounds. • Production of some volatiles increased with the cell permeabilization treatments. • S. cerevisiae and Z. rouxii showed an effect on the production of aromatic compound. • The aromatic compounds produce have promising applications in natural flavors.