We have studied how spherical 23 ± 3 nm Au45Ag55 nanoparticles embedded within a silica matrix transform into prolate nanorods and nanowires by irradiating them with swift heavy ions. Samples were irradiated at room temperature and normal incidence with 74 MeV Kr and 36 MeV S ions for fluences up to 1.0 × 1015 cm−2. We demonstrate the existence of two regimes: (i) below a critical fluence, ∼2.0 × 1014 cm−2, the transformation of the spherical nanoparticle into a nanorod is an individual process, i.e. each nanoparticle transforms into a single nanorod; (ii) for larger fluences the transformation from nanorod to nanowire becomes a collective process, i.e. the break up and dissolution of unstable nanorods contribute to the growth of long nanowires. The passage from the first to the second regime can be interpreted in terms of a Rayleigh-like instability under irradiation. The latter becomes active when the diameter of the nanowire approaches its saturation width under irradiation. Furthermore, we show that the composition of the alloy is only slightly modified during the ion-shaping process. Finally, the energy and the fluence thresholds for deformation and the deformation strain-rate are estimated.