We report the effects of ion-beam bombardment on the room temperature and low temperature magnetic properties of ferromagnetic CoFe/antiferromagnetic (Co,Fe)O thin film bilayers. The films were deposited onto amorphous SiO2 and single crystalline MgO (110)/(100) substrates. Magnetometry showed that ion-beam bombardment was capable of modifying the coercivity and loop shape for the thin film system at room temperature, corresponding to alteration of the effective magneto-crystalline anisotropy field. After field cooling to 50 K, a shifted hysteresis loop was seen for those films containing a proportion of the antiferromagnetic rock-salt (Co,Fe)O phase, with an exchange bias magnitude that depended on the ion-beam bombardment conditions. Our results indicate that matching the substrate with appropriate ion-bombardment conditions provides a promising way to engineer selectively two important types of magnetic anisotropy in ferromagnetic/antiferromagnetic bilayers: magneto-crystalline and exchange bias.