ATP synthases are rotary engines which use the energy stored in a transmembrane electrochemical gradient of protons or sodium ions to catalyze the formation of ATP by ADP and inorganic phosphate. Current models predict that protonation/deprotonation of specific amino acids of the rotating c-ring, extracting protons from one side and delivering them to the other side of the membrane, are at the core of the proton translocation mechanism of these enzymes. In this minireview, an alternative proton binding mechanism is presented, considering hydronium ion coordination as proposed earlier. Biochemical data and structural considerations provide evidence for two different proton binding modes in the c-ring of H+-translocating ATP synthases. Recent investigations in several other proton translocating membrane proteins suggest, that hydronium ion coordination by proteins might display a general principle which was so far underestimated in ATP synthases.