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The prevailing view about molecular catalysts is that the central metal ion is responsible for the reaction mechanism and selectivity, whereas the ligands mainly affect the reaction kinetics. Here, we question this paradigm and show that ligands have a dramatic influence on the selectivity of the product. We show how even a seemingly small change in ligand isomerization sharply alters the selectivity of the well‐researched oxygen reduction reaction (ORR) Co phthalocyanine catalyst from an indirect 2e− to a direct 4e− pathway. Detailed analysis reveals that intramolecular hydrogen‐bond interactions in the ligand activate the catalytic Co, directing the oxygen binding and thus deciding the final product. The resulting catalyst is the first example of a Co‐based molecular catalyst catalyzing a direct 4e− ORR via ligand isomerization, for which it shows an activity close to the benchmark Pt in an actual H2−O2 fuel cell. The effect of the ligand isomerism is demonstrated with different central metal ions, thus highlighting the generalizability of the findings and their potential to open new possibilities in the design of molecular catalysts. [ABSTRACT FROM AUTHOR]