The catalytic performance of extended and nanometer-sized surfaces strongly depends on the amount and the nature of structural defects that they exhibit. However, whereas the effect of steps or adatoms may be unraveled with single crystals (“surface science approach”), implementing reproducibly in a controlled manner structural defects on nanomaterials remains hardly feasible. A case that deserves particular attention is that of bimetallic nanomaterials, which are used to catalyze the oxygen reduction reaction (ORR) in proton exchange membrane fuel cells (PEMFC). Point defects (vacancies), planar defects (dislocations and grain boundaries), and bulk defects (voids, pores) are likely to be generated in alloy or core@shell nanomaterials based on Pt and a transition metal due to the high lattice mismatch between the two elements. Here, we report the morphological and structural trajectories of hollow PtNi/C nanoparticles during thermal annealing under vacuum, N2, H2, or air atmosphere by in situ transmission electron microscopy and synchrotron X-ray diffraction. We evidence atmosphere-dependent restructuring kinetics, which enabled us to synthesize a set of catalysts with identical chemical compositions and elemental distributions but different morphologies, crystallite sizes, and lattice strain. By combining the results of Rietveld and pair-distribution function analyses and electrochemical measurements, we demonstrate that the structurally disordered areas located at the interface between individual crystallites are highly active for two reactions of interest for PEMFC devices: the electrochemical COads oxidation and the ORR. These results shed fundamental light on the effect of structural defects on the catalytic performance of bimetallic nanomaterials and should aid in the rational design of more efficient ORR electrocatalysts.