We report an in situ, temperature and H2 pressure-dependent, characterization of (2.6 ± 0.4) nm palladium nanoparticles supported on active carbon during the process of hydride phase formation. For the first time the core–shell structure is highlighted in the single-component particles on the basis of a different atomic structure and electronic configurations in the inner “core” and surface “shell” regions. The atomic structure of these particles is examined by combined X-ray powder diffraction (XRPD), which is sensitive to the crystalline core region of the nanoparticles, and by first shell analysis of extended X-ray absorption fine structure (EXAFS) spectra, which reflects the averaged structure of both the core and the more disordered shell. In the whole temperature range (0–85 °C), XRPD analysis confirms the existence of two well-separated α- and β-hydride phases with the characteristic flat plateau in the phase transition region of the pressure-lattice parameter isotherms. In contrast, first shell interatomic distances obtained from EXAFS exhibit a slope in the phase transition region, typical for nanostructured palladium. Such difference is explained by distinct properties of bulk “core” which has crystalline structure and sharp phase transition, and surface “shell” which is amorphous and absorbs hydrogen gradually without forming distinguishable α- and β-phases. Combining EXAFS and XRPD we extract, for the first time, the Pd–Pd first-shell distance in the amorphous shell of the nanoparticles, that is significantly shorter than in the bulk core and relevant in catalysis. The core/shell model is supported by the EXAFS analysis of the higher shells, in the frame of the multiple scattering theory, showing that the evolution of the third shell distance (ΔR 3/R 3) is comparable to the evolution of (Δa/a) obtained from XRPD since amorphous PdH x shell gives a negligible contribution in this range of distances. This operando structural information is relevant for the understanding of structure-sensitive reactions. Additionally, we demonstrate the differences in the evolution of the thermal parameters obtained from EXAFS and XRPD along the hydride phase formation.