Atomically precise thiolate-gold nanoclusters with well-defined structures attract attention for use in various applications. However, most of the recently reported synthetic methods rely on prolonged synthesis times (a few hours to days) in order to produce high purity materials with a single cluster size. Such extended synthesis times make these processes ill-suited for adaptation to industrial scale production with continuous flow. In this work, an improved method for the synthesis of thiolated Au₂₅ nanoclusters is presented utilising a microfluidic system and CO-mediated reduction. The optimized system, based on a coiled flow inverter with inner diameter of 1 mm operating at 80 °C and 500 kPa took only 3 min for the synthesis of atomically precise cysteine-capped [Au₂₅(Cys)₁₈] nanoclusters, as characterized by ultraviolet–visible spectroscopy and electrospray ionization mass spectrometry. The productivity of the system was increased by using higher reactant concentrations which led to a throughput of 0.9 g_Au per day, without changing the reaction time or affecting the product purity. The Au nanoclusters were used as photobactericidal enhancement materials. In antimicrobial testing against S. aureus, encapsulation of the Au nanoclusters into crystal violet impregnated silicone showed high photobactericidal activity (~1.7 log reduction in viable bacteria) upon 6 h illumination of white light at ~312 lx, while crystal violet did not show significant photobactericidal activity on its own.