Proton conducting membranes based on a perfluorinated copolymer with short side chains (of the Aquivion® type) are promising for the use in hydrogen fuel cells and overcome in characteristics traditionally used long-chain membranes of the Nation® type. To improve the characteristics of Aquivion® membranes, we used modifying additives in the form of functionalized nanodiamonds. The mechanism of proton conductivity of composite membranes with nanodiamonds is modified by introducing additional ionogenic groups into the structure on the surface of nanodiamonds. The dependences of the conductivity and mechanical properties of the prepared composite membranes on the sign of the surface charge of the introduced nanodiamonds are examined.