Coordination states of metal‐organic materials are known to dictate their physicochemical properties and applications in various fields. However, understanding and controlling coordination sites in metal‐organic systems is challenging. Herein, we report the synthesis of site‐selective coordinated metal‐phenolic networks (MPNs) using flavonoids as coordination modulators. The site‐selective coordination was systematically investigated experimentally and computationally using ligands with one, two, and multiple different coordination sites. Tuning the multimodal Fe coordination with catechol, carbonyl, and hydroxyl groups within the MPNs enabled the facile engineering of diverse physicochemical properties including size, selective permeability (20–2000 kDa), and pH‐dependent degradability. This study expands our understanding of metal‐phenolic chemistry and provides new routes for the rational design of structurally tailorable coordination‐based materials.