A method for obtaining composite gas-diffusion PdCu–Nb–PdCu membranes modified with a nanostructured crystalline coating was developed to increase the performance of Nb-based membranes. A modifying functional layer with a controlled size and composition was synthesized by electrochemical deposition, which made it possible to determine a certain geometric shape for palladium nanocrystallites. Developed PdCu–Nb–PdCu membranes have demonstrated flux values up to 0.232 mmol s−1 m−2 in the processes of diffusion purification of hydrogen at 400 °C. A very significant difference in the hydrogen fluxes through the modified and non-modified composite PdCu–Nb–PdCu membranes reached 1.73 times at the lower threshold temperature of 300 °C. Cu doping of protective layer did not affect the selective properties of the membranes, which was confirmed by the obtained high selectivity values up to 1323, and made it possible to reduce the noble metal content. The research data indicate that the modification of the membrane surface significantly accelerates the hydrogen transfer process at sufficiently low temperatures due to the acceleration of dissociative–associative processes on the surface. The reported approach demonstrates new possibilities for creating productive and cost-efficient membranes based on niobium.