Core-shell nanoparticles are promising candidates for theranostic drugs, as they combine different intrinsic properties with a small size and large surface area. However, their controlled synthesis, or the screening and optimization of synthesis conditions are often difficult and labor intensive. Through the precise control over mass and heat transfer, and automatization possibilities, microfluidic devices could be a solution to this problem in a lab scale synthesis. Here, we demonstrate a microfluidic, capillary, droplet reactor for the multi-step synthesis of iron oxide/gold core-shell nanoparticles. Through the integration of a transmission measurement at the outlet of the reactor, synthesis results can be monitored in a real-time manner. This allowed for the implementation of an optimization algorithm. Starting from three separate initial guesses, the algorithm converged to the same synthesis conditions in less than 30 minutes for each initial guess. These conditions resulted in diameter for the iron oxide core of 5.8 ± 1.4 nm, a thickness for the gold shell of 3.5 ± 0.6 nm, and a total diameter of the core-shell particles of 13.1 ± 2.5 nm. Finally, applications of the iron oxide/gold core-shell nanoparticles were demonstrated for Surface Enhanced Raman Spectroscopy (SERS), photothermal therapy, and magnetic resonance imaging (MRI).