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Abstract Hydrogen fuel cells and electrolyzers operating below 600 °C, ideally below 400 °C, are essential components in the clean energy transition. Yttrium‐doped barium zirconate BaZr_0.8Y_0.2O_3‐d(BZY) has attracted a lot of attention as a proton‐conducting solid oxide for electrochemical devices due to its high chemical stability and proton conductivity in the desired temperature range. Grain interfaces and topological defects modulate bulk proton conductivity and hydration, especially at low temperatures. Therefore, understanding the nanoscale crystal structure dynamics in situ is crucial to achieving high proton transport, material stability, and extending the operating range of proton‐conducting solid oxides. Here, Bragg coherent X‐ray diffractive imaging is applied to investigate in situ and in 3D nanoscale dynamics in BZY during hydration over 40 h at 200 °C, in the low‐temperature range. An unexpected activity of topological defects and subsequent cracking is found on a nanoscale covered by the macroscale stability. The rearrangements in structure correlate with emergent regions of different lattice constants, suggesting heterogeneous hydration. The results highlight the extent and impact of nanoscale processes in proton‐conducting solid oxides, informing future development of low‐temperature protonic ceramic electrochemical cells.