The synthesis of N-methylmorpholine N-oxide by oxidation of N-methylmorpholine with hydrogen peroxide was implemented in a microstructured reactor for increased safety and larger-scale applications. The active oxidant, peroxymonocarbonate HCO₄⁻ is formed in situ from the equilibrium reaction of hydrogen peroxide and bicarbonate. The bicarbonate can be induced by hydration of carbon dioxide. Elaborate studies on the influence of the catalyst concentration and temperature were carried out and the observed activation energy was determined. Elevated temperatures up to 60 °C and a carbon dioxide concentrations of 1 wt% led to a conversion for N-methylmorpholine of approximately 98% within 13.90 min. The used microstructured reactor is designed for process development and intensification and can be applied in the scale-up process to small-scale commercial production. The atom-economic synthesis of N-methylmorpholine N-oxide under flow conditions in such reactors is a safe and beneficial alternative to commercial batch processes.