In this study, we aimed to design and research proton-conducting membranes based on Aquivion®-type material that had been modified with detonation nanodiamonds (particle size 4–5 nm, 0.25–5.0 wt. %). These nanodiamonds carried different functional groups (H, OH, COOH, F) that provided the hydrophilicity of the diamond surface with positive or negative potential, or that strengthened the hydrophobicity of the diamonds. These variations in diamond properties allowed us to find ways to improve the composite structure so as to achieve better ion conductivity. For this purpose, we prepared three series of membrane films by first casting solutions of perfluorinated Aquivion®-type copolymers with short side chains mixed with diamonds dispersed on solid substrates. Then, we removed the solvent and the membranes were structurally stabilized during thermal treatment and transformed into their final form with –SO3H ionic groups. We found that the diamonds with a hydrogen-saturated surface, with a positive charge in aqueous media, contributed to the increase in proton conductivity of membranes to a greater rate. Meanwhile, a more developed conducting diamond-copolymer interface was formed due to electrostatic attraction to the sulfonic acid groups of the copolymer than in the case of diamonds grafted with negatively charged carboxyls, similar to sulfonic groups of the copolymer. The modification of membranes with fluorinated diamonds led to a 5-fold decrease in the conductivity of the composite, even when only a fraction of diamonds of 1 wt. % were used, which was explained by the disruption in the connectivity of ion channels during the interaction of such diamonds mainly with fluorocarbon chains of the copolymer. We discussed the specifics of the mechanism of conductivity in composites with various diamonds in connection with structural data obtained in neutron scattering experiments on dry membranes, as well as ideas about the formation of cylindrical micelles with central ion channels and shells composed of hydrophobic copolymer chains. Finally, the characteristics of the network of ion channels in the composites were found depending on the type and amount of introduced diamonds, and correlations between the structure and conductivity of the membranes were established.