Material selective sensitivity of a magneto-optical polar Kerr effect to magnetic contributions from different inclusions in self-organized magnetic nanostructures is presented. The method is supported by modeling of the magneto-optic response based on the effective medium approximation and by hysteresis loop measurement of the multiferroic BiFeO3–CoFe2O4 self-assembled nanostructure. Magneto-optic selective sensitivity is demonstrated and explained as an effect of different complex diagonal and off-diagonal permittivity tensor elements of two materials.