Hydrogen bonding within the secondary coordination sphere plays a crucial role in tuning the properties of metal complexes. Inspired by nature’s use of flavins in electron transfer processes, we developed a flavin-based bidentate ligand (L) designed to facilitate hydrogen bonding interactions in transition metal coordination. Coordination with first-row transition metals, ranging from manganese to zinc, regioselectively formed stable octahedral 2:1 ligand-to-metal complexes, where two chloride ions engaged in hydrogen bonding. Notably, L exhibited an unusual coordination mode, demonstrating its versatility as a ligand scaffold. In the case of iron, complexation with different (pseudo)halides led to variations in hydrogen bonding interactions within the coordination sphere. Furthermore, ligand tautomerization was induced upon the addition of a base, leading to the formation of a water-coordinated Fe(II) complex. This tautomerization event reorganized the hydrogen bonding network, allowing the nitrogen sites of L to act as both hydrogen bond donors and acceptors. As a result, the ligand exhibited the ability to selectively capture external substrates through the switchable noncovalent interactions. This study highlights the potential of flavin derivatives as versatile ligand platforms for constructing tailored coordination environments, offering new opportunities in bioinspired metal complex design.