Noble metal/metal oxide nanostructures are an efficient system in photocatalysis. Continuous and scalable production of advanced particle systems will be a requirement for commercial-scale deployment for many applications, including photocatalysis. In this work, Au/ZnO structures were synthesized in a continuous flow micro-reactor at room temperature and the detailed characteristics of the product indicate a specific cotton ball-like core-shell microstructure that showcases specific advantages compared to traditional batch synthesis methods. The formation pathway of the core-shell Au/ZnO structures is discussed with the pH-dependent speciation diagram, and photocatalytic activity was assessed under simulated sunlight, demonstrating the enhanced performance of the cotton ball-like Au/ZnO microstructures in photocatalytic dye degradation. This work describes the application of microreaction technology in the continuous production of metal/metal oxide photocatalysts.