Classical molecular dynamics (MD) simulations are used to investigate the role of phase separation (PS) on the Rayleigh-Plateau (RP) instability. Ni–Ag bulk structures are created at temperatures (2000 K and 1400 K) that generate different PS length scales, λPS, relative to the RP instability length scale, λRP. Rectanguloids are then cut from the bulk structures and patterned with a perturbation of certain amplitude and wavelength, λRP. It is found that when λPS ≪ λRP (2000 K), the patterned rectanguloids break up into nanoparticles in a manner consistent with classical RP theory, whereas when λPS ≪ λRP (1400 K), soluto-capillarity affects the RP instability significantly. Specifically, since Ag has a lower surface energy than Ni, Ag migrates to cover neighboring Ni regions, therefore modifying the RP instability. Thus, we demonstrate that the phase separation length scale of an immiscible alloy can be exploited to direct the assembly of functional bimetallic alloys.