A cluster deposition method was used to produce films of loosely aggregated nanoclusters (NC) of Fe core-Fe 3 O 4 shell or fully oxidized Fe 3 O 4 . Films of these NC on Si(100) or MgO(100)/Fe 3 O 4 (100) were irradiated to 10 16 Si 2+ /cm 2 near room temperature using an ion accelerator. Ion irradiation creates structural change in the NC film with corresponding chemical and magnetic changes which depend on the initial oxidation state of the cluster. Films were characterized using magnetometry (hysteresis, first order reversal curves), microscopy (transmission electron, helium ion), and x-ray diffraction. In all cases, the particle sizes increased due to ion irradiation, and when a core of Fe is present, irradiation reduces the oxide shells to lower valent Fe species. These results show that ion irradiated behavior of the nanocluster films depends strongly on the initial nanostructure and chemistry, but in general saturation magnetization decreases slightly.