Caffeine is a molecule with bioactive properties related to increased mental performance. Its use in food products is limited by its bitterness and self-association behavior. The complex formed by β-lactoglobulin and caffeine was characterized by fluorescence spectroscopy, isothermal titration calorimetry, and molecular docking. Fluorescence spectroscopy revealed that β-lactoglobulin interacted with caffeine to form a 1:1 stoichiometric complex. Isothermal titration calorimetry characterization of β-lactoglobulin-caffeine binding revealed a different stoichiometry (1:3). Molecular docking analysis confirmed the information obtained by the two thermodynamic evaluation techniques, showing that the best interaction occurred in the hydrophobic cavity of β-lactoglobulin. The effect of protein conformation was also evaluated by fluorescence spectroscopy. The complex stoichiometry and binding constants were from the same order as those obtained for native β-lactoglobulin. However, in contrast to the complex formation with native protein, the flexibility increase observed in the thermal unfolded protein promoted a great temperature effect on the standard enthalpy and entropy changes of interaction, indicating the presence of a balance between hydrophobic and hydrophilic forces.