The ability to design synthesis processes that are out of equilibrium has opened the possibility of creating nanomaterials with remarkable physico-chemical properties, choosing from a much richer palette of possible atomic architectures compared to equilibrium processes in extended systems. In this work, we employ atomistic simulations to demonstrate how to control polymorph selection via cooling rate during nanoparticle freezing in the case of Ni3Al, a material with a rich structural landscape. State-of-the-art free-energy calculations allow to rationalize the complex nucleation process, discovering a switch between two kinetic pathways, yielding the equilibrium structure at room temperature and an alternative metastable one at higher temperature. Our findings address the key challenge in the synthesis of nano-alloys for technological applications, i.e., rationally exploiting the competition between kinetics and thermodynamics by designing a treatment history that forces the system into desirable metastable states.