In order to improve the understanding of the microscopic phenomena occurring during irradiation in zirconium alloys, ion beam irradiations are performed at 350 DC (dose-rate of 2 × 10-5 dpa/s) on recrystallized Zy-4 and M5 alloys, with 2 MeV protons. The aim of this study is to determine in which way proton irradiations can be representative of neutron irradiations, considering the second phase particle changes and the influence of these changes on the microstructural evolution of the material during irradiation. The 2 MeV proton irradiation at 350 DC, performed here, seems to reproduces well what happened in Zy-4 in PWR conditions with a progressive amorphisation of the Zr(Fe,Cr)2 Laves phases, but with a lower growth rate and a higher Fe/Cr ratio of the amorphous rim. The Zr(Fe,Nb)2 s phase particles in M5 undergo a uniform amorphisation, while the native βNb precipitates remain fully crystalline as evidenced in neutron irradiation at very low irradiation temperature. No radiation-enhanced precipitation of nanometric BETA-Nb particles was observed. Thus, for M5 alloy, the present irradiation seems to be representative of neutron irradiations at a very low irradiation temperature. Nevertheless it does not reproduce what happens in PWR conditions, where no amorphisation and a drastic loss of iron is reported for the Zr(Fe,Nb)2 Laves phase SPPs. Despite the lower iron rejection from the particles into the matrix during proton irradiation than during neutron irradiation, -component loop distribution is found to be similar after both types of irradiations. These results underline the influence of both dose-rate and temperature on second phase particles behavior under irradiation and point out the complexity of iron rejection influence on the basal -component loops. Indeed, although the -component loop nucleation and growth seem locally correlated to iron dissolution into the matrix, they do not seem to be directly correlated to the global amount of iron rejected.