The first direct aza-Diels–Alder reaction catalyzed using phosphotungstic acid combined with a water absorption device in a micro-flow system was reported. The optimization process gave azabicyclo[2.2.2]octan-5-ones in 98.78% conversion and an endo/exo ratio of 7/93. Exo cycloadducts were quickly prepared due to efficient mixing and heat transfer in the micro-flow system. However, exo products could be turned into endo cycloadducts which were more stable.