We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna–Matthews–Olson (FMO) protein by using a polarizable MM model combined with a time‐dependent density functional theory description. Overall, our results indicate that structural fluctuations, electrostatic interactions, and short‐range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). We find that the specific interactions with the axial ligand and the hydrogen‐bonded residues are responsible for the energy ladder, with their effects being mainly due to electrostatic interactions, but with short‐range quantum contributions that are not negligible. In addition, a striking modulation of the screening effects experienced by the BChl pairs, due to the heterogeneous polarizability of the FMO and solvent environment, is observed. Finally, we find that the exciton model gives a reliable description of the delocalized excited states in the complex.