Abstract Green coffee beans (GCB) (Coffea arabica L.) contain phenolic compounds with proven antioxidant capacity. GCB fermentation by Aspergillus oryzae was focused on the biotransformation of phenolic compounds into smaller molecules targeting a greater skin penetration. GCB was fermented under solid state for 24, 36, and 48 h and the phenolics were extracted using a hydroethanolic solution (ethanol/water 80:20, v/v). The antioxidant activity of the extracts was evaluated by 2,2-diphenyl-1-picryl-hydrazyl spectrophotometric and thin layer chromatography methods. HPLC and UPLC-MS-Q-TOF were used for chemical characterization. Gel creams containing 5% of lyophilized non-biotransformed and biotransformed (36 h) GCB extracts were submitted to in vitro skin penetration studies. Chromatographic analyzes showed qualitative and quantitative changes in the chemical composition of GCB after biotransformation. Caffeoylquinic and feruloylquinic acid derivatives as well as quinic and caffeic acids and caffeine were the major bioactive compounds identified. It was evidenced the breakage of chlorogenic acid ester bonds mainly after 36 h of fermentation without loss of the antioxidant activity. In vitro penetration studies showed no penetration of phenolic compounds. Caffeine was the only compound able to penetrate in skin, and the penetration was higher when the formulation was incorporated by the extract of CGB biotransformed for 36 h in comparison with the non-biotransformed. Our results reinforce the importance of the skin penetration studies to guarantee the efficacy of pharmaceutical and cosmetic formulations containing these ingredients, since this study has been shown that a commonly used formulation has not been able to promote the penetration of the active compounds into the skin.