The potential of the two-color mode implemented at the FERMI free-electron laser (FEL) source for pumping and probing selectively different atomic species has been demonstrated by time-resolved scattering experiments with permalloy (FeNi alloy) and NiFe2O4 samples. We monitored the ultra-fast demagnetization of Ni induced by the pump FEL pulse, by tuning the linearly-polarized FEL probe pulse to the Ni-3p resonance and measuring the scattered intensity in the transverse magneto-optical Kerr effect geometry. The measurements were performed by varying the intensity of the FEL pump pulse, tuning its wavelength to and off of the Fe-3p resonance, and by spanning the FEL probe pulse delays across the 300-900 fs range. The obtained results have evidenced that for the case of NiFe2O4, there is a sensible difference in the magnetic response at the Ni site when the pump pulse causes electronic excitations at the Fe site.