AbstractThe site‐selective modification of complex biomolecules by transition metal‐catalysis is highly warranted, but often thwarted by the presence of Lewis basic functional groups. This study demonstrates that protonation of amines and phosphates in carbohydrates circumvents catalyst inhibition in palladium‐catalyzed site‐selective oxidation. Both aminoglycosides and sugar phosphates, compound classes that up till now largely escaped direct modification, are oxidized with good efficiency. Site‐selective oxidation of kanamycin and amikacin was used to prepare a set of 3’‐modified aminoglycoside derivatives of which two showed promising activity against antibiotic‐resistant E. coli strains.