Palladium nanoparticles offer an attractive alternative to bulk palladium for catalysis, hydrogen storage and gas sensing applications. Their performance depends strongly on surface structure; therefore, nanoparticle coalescence can play an important role, as it determines the resultant structure of the active sites where reactions (e.g. catalysis) actually take place, i.e. facets, edges, vertices or protrusions. With this in mind, we performed classical molecular dynamics (MD) simulations and magnetron-sputtering inert gas condensation depositions of palladium nanoparticles, supported by high-resolution transmission electron microscopy (HRTEM), to study the mechanisms that govern their coalescence. Surface energy minimisation drove the interactions initially, leading to the formation of an interface/neck, as expected. Intriguingly, at a later stage, atomic rearrangements triggered a crystallisation wave propagating through the amorphous nanoparticles, leading to mono- or polycrystalline fcc structures. In the case of crystalline nanoparticles, almost-epitaxial alignment occurred and the formation of twins and surface protrusions were observed.