The development of stimuli responsive systems that can switch between two distinct spin states under the application of an external stimulus has always remained an elusive challenge. Here, we report a stimuli-based spin filter by utilizing a photo-responsive endoperoxide (EPO) based single molecule device. Photo-irradiation of EPO triggers the homolytic cleavage of the peroxide O–O bond generating a diradical intermediate centered on two O-atoms which facilitates high spin filtering efficiency when placed between gold electrodes. The broken conjugated scenario due to the peroxide bridge of EPO hinders the propagation of de Broglie waves across the molecular skeleton. On the other hand, the diradical intermediate of EPO yields high conductance for one of the spin configurations. The transmission characteristics of various photoproducts along the photochemical reaction pathway of EPO are also investigated using density functional theory in combination with the non-equilibrium Green’s function (NEGF-DFT) technique. We demonstrate the key role played by quantum interference (QI) effects in the dramatic modulation of conductance arising due to different degrees of conjugation along the reaction pathway of EPO.