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Layered Na₃Fe₃(PO₄)₄ can function as a positive electrode for both Li- and Na-ion batteries and may hold advantages from both classical layered and phosphate-based electrode materials. Using a combination of ex-situ and operando synchrotron radiation powder X-ray diffraction, void space analysis, and Mössbauer spectroscopy, we herein investigate the structural evolution of the Na₃Fe₃(PO₄)₄ framework during Li- and Na-ion intercalation. We show that during discharge, Li- and Na-intercalation into Na₃Fe₃(PO₄)₄ occurs via a solid solution reaction wherein Na-ions appear to be preferentially intercalated into the intralayer sites. The intercalation causes an expansion of the unit cell volume, however at open circuit conditions after ion-intercalation (i.e., after battery discharge), Na_3+xFe₃(PO₄)₄ and Li_xNa₃Fe₃(PO₄)₄ undergo a structural relaxation, wherein the unit volume contracts below that of the pristine material. Rietveld refinement suggests that the ions intercalated into the intra-layer sites diffuse to the sites in the inter-layer space during the relaxation. This behavior brings new perspectives to understanding structural relaxation and deviations between structural evolution observed under dynamic and static conditions.