Covalent organic frameworks (COFs) are crystalline materials with intrinsic porosity that offer a wide range of potential applications spanning diverse fields. Yet, the main goal in the COF research area is to achieve the most stable thermodynamic product while simultaneously targeting the desired size and structure crucial for enabling specific functions. While significant progress is made in the synthesis and processing of 2D COFs, the development of processable 3D COF nanocrystals remains challenging. Here, a water‐based nanoreactor technology for producing processable sub‐40 nm 3D COF nanoparticles at ambient conditions is presented. Significantly, this technology not only improves the processability of the synthesized 3D COF, but also unveils exciting possibilities for their utilization in previously unexplored domains, such as nano/microrobotics and biomedicine, which are limited by larger crystallites. Herein, a water‐based nanoreactor technology that allows for the controlled generation of sub‐40 nm 3D covalent organic frameworks (COF) nanoparticles, boosting processability, and opening new frontiers in nano/microrobotics and biomedicine is presented. This breakthrough clearly overcomes the limitations posed by larger reported 3D COF crystal structures, unlocking exciting possibilities for previously unexplored domains.