Bimetallic nanostructures are primarily synthesized in small volume batches. However, droplet-based reactors are receiving attention due to their ability to maintain thermal and compositional equilibrium within and between droplets, enabling flow operations for inline analyses and the scale-up of nanomaterial syntheses. Here, the syntheses of shape-controlled core@shell Au@Pd nanostructures with variable shell thicknesses are reported through control of the relative flow rates of reagents within the microreactor. Specifically, Pd shells were grown on cubic or octahedral Au seeds, selected as a model system. In batch reactions, shell thickness is determined by precursor concentration; however, as shown here, precursor feedstock concentration can be held constant, with the precursor concentration within the droplets being controlled through relative flow rates. This approach allows process conditions to be modified inline rather than from batch to batch to achieve particles with different shell thicknesses, and this procedure should be applicable to other multicomponent systems.