Light sensing in photoreceptor proteins is subtly modulated by the multiple interactions between the chromophoric unit and its binding pocket. Many theoretical and experimental studies have tried to uncover the fundamental origin of these interactions but reached contradictory conclusions as to whether electrostatics, polarization, or intrinsically quantum effects prevail. Here, we select rhodopsin as a prototypical photoreceptor system to reveal the molecular mechanism underlying these interactions and regulating the spectral tuning. Combining a multireference perturbation method and density functional theory with a classical but atomistic and polarizable embedding scheme, we show that accounting for electrostatics only leads to a qualitatively wrong picture, while a responsive environment can successfully capture both the classical and quantum dominant effects. Several residues are found to tune the excitation by both differentially stabilizing ground and excited states and through nonclassical “inductive resonance” interactions. The results obtained with such a quantum-in-classical model are validated against both experimental data and fully quantum calculations.