Advances in nanofabrication techniques are undoubtedly needed to obtain nanostructured magnetic materials with physical and chemical properties matching the pressing and relentless technological demands of sensors. Solid-state dewetting is known to be a low-cost and “top-down” nanofabrication technique able to induce a controlled morphological transformation of a continuous thin film into an ordered nanoparticle array. Here, magnetic Fe70Pd30 thin film with 30 nm thickness is deposited by the co-sputtering technique on a monocrystalline (MgO) or amorphous (Si3N4) substrate and, subsequently, annealed to promote the dewetting process. The different substrate properties are able to tune the activation thermal energy of the dewetting process, which can be tuned by depositing on substrates with different microstructures. In this way, it is possible to tailor the final morphology of FePd nanoparticles as observed by advanced microscopy techniques (SEM and AFM). The average size and height of the nanoparticles are in the ranges 150–300 nm and 150–200 nm, respectively. Moreover, the induced spatial confinement of magnetic materials in almost-spherical nanoparticles strongly affects the magnetic properties as observed by in-plane and out-of-plane hysteresis loops. Magnetization reversal in dewetted FePd nanoparticles is mainly characterized by a rotational mechanism leading to a slower approach to saturation and smaller value of the magnetic susceptibility than the as-deposited thin film.