The synthesis, isolation and spectroscopic characterization of holmium-based mixed metal nitride clusterfullerenes HoxSc3−xN@C80 (x=1, 2) are reported. Two isomers of HoxSc3−xN@C80 (x=1, 2) were synthesized by the reactive gas atmosphere method and isolated by multistep recycling HPLC. The isomeric structures of HoxSc3−xN@C80 (x=1, 2) were characterized by laser-desorption time-of-flight (LD-TOF) mass spectrometry and UV/Vis/NIR, FTIR and Raman spectroscopy. A comparative study of MxSc3−xN@C80 (M=Gd, Dy, Lu, Ho) demonstrates the dependence of their electronic and vibrational properties on the encaged metal. Despite the distinct perturbation induced by 4f10 electrons, we report the first paramagnetic 13C NMR study on HoxSc3−xN@C80 (I; x=1, 2) and confirm Ih-symmetric cage structure. A 45Sc NMR study on HoSc2N@C80 (I, II) revealed a temperature-dependent chemical shift in the temperature range of 268–308 K.