In this study, coatings of polydopamine (PDA) in the presence of caffeine were investigated upon their deposition on substrates with different surface energies. The physicochemical properties and stability of PDA coatings deposited in the absence and presence of caffeine (C/PDA) on Si/SiO2 (high surface energy), cellulose acetate butyrate (CAB) (intermediate surface energy) and polystyrene (PS) (low surface energy) surfaces were investigated by means of ellipsometry, contact angle measurements and X-ray photoelectron spectroscopy. In order to gain insight about the interactions between caffeine and PDA at molecular level, Raman and infrared (FTIR-ATR) spectroscopy measurements were performed for PDA and C/PDA, and the results were supported by density functional theory calculations. In comparison with bare PDA, the C/PDA system displayed an increase in the deposition rate on all substrates, indicating co-deposition of caffeine and PDA. PDA and C/PDA coatings turned hydrophobic substrates into hydrophilic surfaces and vice versa. PDA coatings on CAB and PS films were the most stable systems. CAB/PDA microbeads were created and tested as new adsorbents for caffeine, presenting removal capacity of 40%.