Metal-catalyzed hydrothermal deuteration provides a direct and atom-efficient route to hydrogen-deuterium (H/D) exchange using heavy water (D2O), yet conventional batch processing remains limited by poor heat and mass transfer and restricted scalability. Here, we report a continuous-flow deuteration platform that enables tunable and selective isotopic labelling of saturated short-chain fatty acids over platinum-group metal catalysts. Compared with Parr reactors, flow chemistry promotes high steady-state activity, improves single-pass productivity, and provides direct mechanistic insight into isotopologue and isotopomer formation under well-defined reaction conditions. Using butyric acid as a benchmark substrate, platinum catalysts exhibit markedly higher intrinsic activity than palladium and favour perdeuteration under hydrogen-free conditions. Isotopologue and isotopomer analyses reveal that flow deuteration favours rapid (30 – 60 min) and selective formation of thermodynamically stable deuterated products (94%D, 60%-d7, 30%-d6) at elevated temperature (> 200 °C) in single pass, highlighting the role of controlled heat transfer and short diffusion lengths (higher surface area-volume ratio) in directing H/D exchange pathways. Density functional theory calculations support a mechanism dominated by preferential α-C-H activation via cooperative C- and O-metal interactions on platinum surfaces, rationalising the enhanced deuterium incorporation observed under flow. More broadly, this work reinforces the benefits of flow chemistry for deuteration reactions, including safe and robust operation at high temperature and pressure and precise control of reaction conditions. The approach is readily extendable to other short chain carboxylic acids and platform molecules, offering opportunities for the synthesis of deuterated fatty acids, bio-derived building blocks, and isotope-labelled probes for mechanistic, metabolic, and pharmaceutical studies.