Display omitted •Flow synthesis of DAB-TFP COF was achieved at low temperature and in less time than the conventional batch process.•DAB-TFPFlow is highly efficient for the adsorption of methylene blue than DAB-TFPBatch.•In-situ flow adsorption was more effective for the removal of pollutants.•High recyclability and in-situ regeneration of DAB-TFPFlow COF in continuous flow.•The DAB-TFPFlow COF was also effective for the adsorption of simulated textile waste. Covalent organic frameworks (COF) are increasingly gaining attention as adsorbents for industrial pollutants due to their high surface area and ordered porosity. However, often they have low removal efficiency due to the limited access to their pores. Approachability of foreign molecules to active sites within the framework can be maximized by pore engineering and introduction of defects. Here, we report the synthesis of an imine-based COF (DAB-TFP) at ambient conditions with the incorporation of disorder using continuous flow for the first time. A reusable microreactor that was fabricated using a cost-effective scaffolding technique was used for the flow reactions. The disorder in the COF increased accessibility of its surface for foreign molecules. Moreover, the disorder within the COF resulted in accelerated adsorption of methylene blue (MB) in continuous flow. The removal efficiency of the COF for MB was three folds higher during in-situ adsorption in continuous flow than the traditional batch mode of adsorption. The COF could be regenerated and recycled in continuous flow without any significant loss in the activity. Further, almost 100 % of MB could be reclaimed. The COF was also able to efficiently adsorb a mixture of pollutants as well as a simulated textile industrial waste. Hence, the reported method is a green and sustainable approach for industrial effluent treatment.