Magnetite (Fe3O4) and core-shell iron/iron-oxide (Fe/FexOy) nanomaterials prepared by a cluster deposition system were irradiated with 5.5 MeV Si2+ ions and the structures determined by X-ray diffraction as consisting of 100% magnetite and 36/64 wt% Fe/FeO, respectively. However, X-ray magnetic circular dichroism (XMCD) indicates similar surfaces in the two samples, slightly oxidized and so having more Fe3+ than the expected magnetite structure, with XMCD intensity much lower for the irradiated core-shell samples indicating weaker magnetism. X-ray absorption spectroscopy (XAS) data lack a strong signature for FeO, but the irradiated core-shell system consists of Fe-cores with ∼13 nm of separating oxide crystallite, so it is likely that most FeO (octahedral Fe2+) exists deeper than the probe depth of the XAS (∼5 nm). Exchange bias (Hex) for both samples becomes increasingly negative as temperature is lowered, but the irradiated Fe3O4 sample shows greater sensitivity of cooling field on Hex. Loop asymmetries and Hex sensitivities of the irradiated Fe3O4 sample are due to interfaces and interactions between grains, which were not present in samples before irradiation, as well as surface oxidation. Asymmetries in the hysteresis curves of the irradiated core/shell sample are related to the reversal mechanism of the antiferromagnetic FeO and possibly some near surface oxidation.