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Understanding of the protonic defect transport mechanism in Ba(Ce,Zr)O3 perovskite oxides and defining the appropriate temperature range for ionic conductivity are fundamental to material design and application as electrolytes for solid oxide fuels and electrolyzer cells, isotopic separation membranes, and hydrogen sensors. Structural features of the material, and lattice distortions and proton diffusion are key factors that define the protonic conduction. The crystal structure of protonated and deuterated BaCe0.4Zr0.4Y0.2O3-? (BCZY) perovskite and its correlation with protonic transport was studied by in situ neutron powder diffraction (NPD) and complementary thermogravimetry (TG), quasi-elastic neutron scattering (QENS) and isotope exchange depth profiling (IEDP) techniques. A second order phase transition from rhombohedral to cubic symmetry takes place at intermediate temperatures (400-600 °C). Dynamic measurements of NPD allowed the detection of the temperature of the phase transition for BCZY at around 520 °C. Crystallographic and microstructural parameters, including deuterium occupancy and anisotropic thermal parameters, were determined from high resolution NPD data. The deuterium (and oxygen) occupancy for pre-hydrated BCZY was at its maximum at low temperature and decreased at temperatures greater than 400 °C, even through the phase transition and beyond 600 °C. By contrast, proton diffusion increased with temperature above the phase transition. The combination of both effects, i.e., deuterium content and diffusion coefficient, explains the previous results showing that the proton conductivity dominates the ionic conductivity over the oxygen vacancy mechanism until 600 °C. The phase transition is mainly related to oxygen sublattice relaxation and does not impact the protonic transport mechanism.