This paper investigates the role of ion-induced disorder on the morphology and magnetic properties of chemically ordered FePt3films. The effects are studied for 15 keV He+ions as a function of the ion fluence for 0, 2 × 1016and 2 × 1017ions cm−2. Substitutional mixing of the L12-type Fe-Pt sites takes place within the region of the chemically ordered FePt3film affected by the irradiation. This accompanies a paramagnetic-to-ferromagnetic transition, as determined by room-temperature magnetometry. Dark-field transmission electron microscopy (TEM) measurements confirm that the 15 keV He+ions induce a 120 nm-thick chemically disordered layer into the sub-surface region of the nominally 280 nm-thick ordered FePt3film. The average domain size and the fractional density of the chemically ordered domains within the irradiated FePt3microstructure are found to mutually decrease with increasing ion fluence. Selected-area electron diffraction results demonstrate that the film's single crystallinity is preserved after irradiation, irrespective of the ion fluence. High-resolution TEM elucidates the coexistence of ordered domains and precipitate disordered domains in the near-surface, low-ion impacted regions of the FePt3film. Collectively, this work provides detailed insights into the material-science relationship between ion-induced disorder and ferromagnetism in FePt3, as a step towards creating fully customisable, ion-beam-synthesised magnetic nano-elements.