Molecular junctions are formed by wedging molecules between two metal electrodes. In addition to the conventional parameters of the metal–molecule–metal junction, such as the work function of electrodes and the molecules’ energy gap, molecule-electrode electronic coupling strength also plays a vital role in modulating the electronic properties of the molecular junction under external stimuli. We have examined the electron transport across bacteriorhodopsin molecular junction under various external forces applied at the AFM tip in the electrical characterization process with different humidity values under dark and illumination conditions. We have analyzed experimentally obtained I–V data under these external stimuli using tunneling-based transport modeling techniques such as differential conductance, law of corresponding states, normalized differential conductance, transition voltage spectroscopy, and Landauer transport formalism. We have also calculated several transport parameters which play a crucial role in finding the origin of conductance modulation under the external stimuli. We found that before particular humidity conditions, the modulation in the conductance is due to the variation in coupling strength, which is due to the modulation in the electrostatic environment of retinal chromophores of a protein by changing its structure under various external stimuli.