Metal-organic frameworks (MOFs); also known as porous coordination polymers (PCP) are a class of porous crystalline materials constructed by connecting metal clusters via organic linkers. The possibility of functionalization leads to virtually infinite MOF designs using generic modular methods. Functionalized MOFs can exhibit interesting physical and chemical properties including accelerated adsorption kinetics and catalysis. Although there are discrete methods to synthesize well-defined nanoscale MOFs, rapid and flexible methods are not available for continuous, one-pot synthesis and post-synthetic modification (functionalization) of MOFs. Here, we show a continuous, scalable nanodroplet-based microfluidic route that not only facilitates the synthesis of MOFs at a nanoscale, but also offers flexibility for direct functionalization with desired functional groups (e.g., -COCH3, fluorescein isothiocyanate; FITC). In addition, the presented route of continuous manufacturing of functionalized nanosized MOFs takes significantly less time compared to state-of-the-art batch methods currently available (1 hr vs. several days). We envisage our approach to be a breakthrough method for synthesizing complex functionalized nanomaterials (metal, metal oxides, quantum dots and MOFs) that are not accessible by direct batch processing and expand the range of a new class of functionalized MOF-based functional nanomaterials.