Porous superstructures are characterized by a large surface area and efficient molecular transport. Although methods aimed at generating porous superstructures from nanocrystals exist, current state-of-the-art strategies are limited to single-component nanocrystal dispersions. More importantly, such processes afford little control over the size and shape of the pores. Here, we present a new strategy for the nanofabrication of porous magneto-fluorescent nanocrystal superparticles that are well controlled in size and shape. We synthesize these composite superparticles by confining semiconductor and superparamagnetic nanocrystals within oil-in-water droplets generated using microfluidics. The rapid densification of these droplets yields spherical, monodisperse, and porous nanocrystal superparticles. Molecular simulations reveal that the formation of pores throughout the superparticles is linked to repulsion between nanocrystals of different compositions, leading to phase separation during self-assembly. We confirm the presence of nanocrystal phase separation at the single superparticle level by analyzing the changes in the optical and photonic properties of the superstructures as a function of nanocrystal composition. This excellent agreement between experiments and simulations allows us to develop a theory that predicts superparticle porosity from experimentally tunable physical parameters, such as nanocrystal size ratio, stoichiometry, and droplet densification rate. Our combined theoretical, computational, and experimental findings provide a blueprint for designing porous, multifunctional superparticles with immediate applications in catalytic, electrochemical, sensing, and cargo delivery applications.