The structural behavior of the tetragonal NdBaMn₂O₅ phase, a member of the family of A-site ordered layered manganites that have been recently suggested as possible mixed ionic and electronic conductors, has been investigated by means of in situ neutron powder diffraction. Considering applications in energy production and storage devices and use of NdBaMn₂O₅₊δ as an electrode in symmetrical cells, the study was carried out in relevant atmosphere conditions, i.e. dilute hydrogen (wet and dry) and dry air in the temperature range 25–800 °C. Neutron data under flowing hydrogen allowed monitoring of the structural phase transition from the charge-ordered to the charge-disordered state as a function of temperature. Slow reduction of the fully oxidised phase, NdBaMn₂O₆, previously formed from quick oxidation of the pristine material, enabled real-time observation of the intermediate NdBaMn₂O₅.₅ phase and its crystal characterization up to 700 °C in the course of its conversion to NdBaMn₂O₅. Oxygen vacancy ordering within the Nd layers of NdBaMn₂O₅.₅ correlated with antiferrodistortive orbital ordering of the Jahn–Teller Mn³⁺ ion in the square pyramids and octahedra results in large thermal expansion and relatively slow anisotropic oxygen diffusion occurring in the NdO layer. The four heating/cooling cycles evidenced no oxygen miscibility between the three distinct phases detected in the NdBaMn₂O₅₊δ system with δ ∼ 0, 0.5 and 1 and clearly demonstrated that reversible oxygen intercalation/deintercalation underpins the phase stability of the LnBaMn₂O₅₊δ materials to redox cycling and to wet atmosphere in high temperature electrochemical devices.