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The traditional batch production of blocked polyisocyanates, key components in the preparation of self-cross-linking resins, has significant drawbacks associated with the exothermic character of the reaction and the high viscosity of some of the materials involved. We have developed a continuous flow strategy for the generation of a methyl ethyl ketoxime-blocked polyisocyanate. The neat oxime and the viscous polyisocyanate were pumped and mixed in continuous flow using a Kenics static mixer. The homogeneous mixture obtained was fully converted to the target blocked polyisocyanate in a residence time unit downstream of the mixer. Real-time reaction monitoring, via in-line Fourier-transform infrared analysis at the reactor outlet, has been implemented, enabling fast optimization of the reaction conditions and providing a sensitive and reliable method to control product quality. The process has been intensified in flow by stepwise increase of the temperature of the residence time unit. Full conversion after only 15 s of overall residence time has been achieved at 155 °C, providing a productivity of ca. 1 kg per hour for a reactor of only 4.5 mL volume. The ecological impacts of a conceptualized upscaled flow process compared to the industrial batch procedure have been evaluated by a comparative life cycle assessment (LCA) according to the ISO 14040/44 LCA framework. The LCA results illustrate the capabilities of continuous processing to enable more sustainable production of blocked polyisocyanates.