We report the formation of self-assembled monolayers of a molecular photoswitch (azobenzene-bithiophene derivative, AzBT) on cobalt via a thiol covalent bond. We study the electrical properties of the molecular junctions formed with the tip of a conductive atomic force microscope under ultra-high vacuum. The statistical analysis of the current-voltage curves shows two distinct states of the molecule conductance, suggesting the coexistence of both the trans and cis azobenzene isomers on the surface. The cis isomer population (trans isomer) increases (decreases) upon UV light irradiation. The situation is reversed under blue light irradiation. The experiments are confronted to first-principle calculations performed on the molecular junctions with the Non-Equilibrium Green’s Function formalism combined with Density Functional Theory (NEGF/DFT). The theoretical results consider two different molecular orientations for each isomer. Whereas the orientation does not affect the conductance of the trans isomer, it significantly modulates the conductance of the cis isomer and the resulting conductance ON/OFF ratio of the molecular junction. This helps identifying the molecular orientation at the origin of the observed current differences between the trans and cis forms. The ON state is associated to the trans isomer irrespective of its orientation in the junction, while the OFF state is identified as a cis isomer with its azobenzene moiety folded upward with respect to the bithiophene core. The experimental and calculated ON/OFF conductance ratios have a similar order of magnitude. This conductance ratio seems reasonable to make these Co-AzBT molecular junctions a good test-bed to further explore the relationship between the spin-polarized charge transport, the molecule conformation and the molecule-Co spinterface.