Molecules chemically synthesized as periodic two-dimensional (2D) frameworks via covalent bonds can form some of the highest-surface area and -charge density particles possible. There is significant potential for applications such as nanocarriers in life sciences if biocompatibility can be achieved; however, significant synthetic challenges remain in avoiding kinetic traps from disordered linking during 2D polymerization of compatible monomers, resulting in isotropic polycrystals without a long-range order. Here, we establish thermodynamic control over dynamic control on the 2D polymerization process of biocompatible imine monomers by minimizing the surface energy of nuclei. As a result, polycrystal, mesocrystal, and single-crystal 2D covalent organic frameworks (COFs) are obtained. We achieve COF single crystals by exfoliation and minification methods, forming high-surface area nanoflakes that can be dispersed in aqueous medium with biocompatible cationic polymers. We find that these 2D COF nanoflakes with high surface area are excellent plant cell nanocarriers that can load bioactive cargos, such as the plant hormone abscisic acid (ABA) via electrostatic attraction, and deliver them into the cytoplasm of intact living plants, traversing through the cell wall and cell membrane due to their 2D geometry. This synthetic route to high-surface area COF nanoflakes has promise for life science applications including plant biotechnology.