Femtosecond laser irradiation in Au@Ag, Ag@Au core@shell, and Au–Ag Janus-like nanoparticles are investigated using molecular dynamics simulations. Our results show that the morphology of Au@Ag core–shell and Au–Ag Janus-like nanoparticles tend to form hollow-like nanostructures due to the ultrafast energy transfer and the subsequent cooling process. In contrast, our results also shows that Ag@Au nanoparticles do not form a hollow structure due to the high diffusion of Ag atoms and the limited expansion of the Au shell. Besides, successive laser impacts on the Au–Ag Janus-like nanoparticle produce a structure that alternates from hollow to a solid nanoparticle and, at the same time, promotes atomic diffusion, favoring the alloying process of the Ag and Au atoms. In addition, the evolution of the crystalline structure is studied, observing a saturation of the planar defects due to the impossibility of forming a new crystalline phase. The energy variation between the initial and final step, it is not influenced by the presence of the hollow, however it is dominated by the increase of planar defects.