Covalent organic frameworks (COFs) are an attractive class of crystalline, porous materials because their reticular chemistry allows frameworks to be synthesized in a predictable manner. As a result of this defining characteristic, the past decades have witnessed considerable efforts to demonstrate unique pore shapes and sizes; however, less attention is often given to atomistic level structural changes. To further understand the relationship of a COF’s structure and its unique properties, this work provides a foundational study exploring the relationship of structural isomer linkages in two COFs, TAPA–PDA COF and IISERP-COF2. These imine-based COFs were extensively studied and compared with respect to their synthetic conditions, framework properties, phase reversibility, optical properties, and surface energy. Our results suggest that compared to IISERP-COF2, the TAPA–PDA COF has stronger phase change reversibility and significant red shifting of the UV–vis absorption and fluorescence and exhibits hydrophilicity. These findings provide evidence that careful consideration of monomer pairs is necessary when designing materials because these minor structural changes can lead to vastly diverging properties.

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