Nature can precisely control the assembly and growth of crystalline structures across scales, from the nano-to the millimeter scale, to achieve materials with targeted functions while using only a limited selection of components and/or building blocks. Despite the significant progress made by the scientific community in the development of crystalline synthetic materials, the methods and technologies used still pale in comparison to the workings of nature. For instance, most attempts made at controlling the assembly, size, and function of human-made crystalline materials have been based on Edisonian experimentation, in which parameters such as the molecular design, solvent, temperature, catalyst concentration, and/or monomer composition are varied individually, and in discrete steps, to achieve the most stable thermodynamic product, striving for the desired size and structure, both of which are crucial for enabling a specific function. Covalent organic frameworks (COFs) stand as an outstanding showcase of these humanengineered crystalline materials and underlying Edisonian approach. COFs are porous crystalline structures assembled in 2D and 3D through covalent bonds. Note that when crystals are solely grown from covalent bonds, they often yield kinetically trapped disordered structures. To avoid this, solvothermal conditions and reversible covalent bonds have become prevalent in the COF field to foster the generation of porous crystalline thermodynamic products. Yet, however, COF synthesis methods often rely on the use of hazardous or toxic solvents as reaction media, where the solubility of the building blocks is severely limited. This limitation frequently results in the formation of irregular and unprocessable microcrystalline powders where the control over their morphology and size is greatly hampered. While significant advancements have been made in the synthesis and processing of 2D COFs by effectively controlling their formation across various scales , the development of 3D COF crystals of varying sizes is still challenging, significantly impeding their processability and constraining their widespread application beyond the realms of catalysis and adsorption. Recently, the use of modulators during the synthesis of 3D COFs enabled the generation of single crystals measuring several tens of micrometers in size. This innovative approach demonstrated that modulators can effectively inhibit the rapid nucleation of 3D COFs and concurrently act as error-correction moieties during crystal growth, enabling the generation of large single crystals suitable for single-crystal X-ray diffraction analysis. Yet, this synthetic approach relies on harsh conditions that hinder the controlled assembly of these materials at the nanoscale, which is crucial for improving their processability and seamless integration into micrometric structures. To the best of our knowledge, no existing methodologies have been reported so far that can achieve the controlled assembly of 3D COFs at the nanoscale and under mild conditions. Such advancements are not only expected to enhance their processability, but also open new opportunities for the application of these functional materials in other fields such as nano/microrobotics and biomedicine. Herein, we present a water-based nanoreactor technology for producing processable sub-40 nm 3D COF nanoparticles at room temperature and atmospheric pressure. This technology relies on a micellar approach that guarantees the solubility of the 3D COF precursors in water. Our findings showcase that employing this approach allows for an in-depth examination of the growth mechanism of a 3D COF, and it also enables the production of a final colloidal solution that can be directly utilized for functionalizing intricate micron-sized structures with 3D COF nanoparticles, all in a convenient one-pot process.