Abstract Three‐dimensional covalent organic frameworks (3D COFs) are notably crystalline and stable, but their architectures and monomer structures make them difficult to functionalize. Here, a new strategy is presented to render COF‐300 and other imine‐linked frameworks amenable to facile functionalization in the last step of synthesis. By reducing the imine linkages to secondary amines and appending them with acetyl halide groups, the linkages are converted to electrophiles that can be readily reacted with nucleophilic guests. This route yields eight new COF‐300 derivatives, bearing chloroacetyl, bromoacetyl, azide, cyano, amino, hydroxyl, methoxy, or thiomethyl groups appended to the inter‐monomer linkages. The new materials are characterized through solid‐state NMR, infrared spectroscopy, and powder X‐ray diffraction, among other techniques, finding that the reported linkage transformations proceed to complete conversion while retaining the crystallinity of the materials. Microcrystal electron diffraction (microED) data are used to solve the evacuated structure of the amine‐linked framework COF‐300‐AR for the first time, providing conclusive evidence of this framework's guest‐induced phase change, along with the structure of the new framework COF‐300‐NH 2 . Finally, COF‐300‐NH 2 is shown to have significantly improved adsorption capacity for CO 2 and perfluoroalkyl substances (PFAS), highlighting the benefits of this synthetic strategy for the generation of customized adsorbents.