The structures of the ordered and isotype oxyfluorides NaMO2F2 (M = Nb, Ta) were thoroughly investigated by combining powder X-Ray Diffraction (PXRD), 19F and high-field 23Na and 93Nb solid-state NMR, and DFT calculations. The structures, derived from Rietveld refinement of the PXRD data, exclusively consist of cis-[MO4F2]5– octahedra, in which cations are displaced from their ideal centered positions toward an oxide face. The NMR parameters were calculated for both the experimental (ES) and the atomic positions optimized (APO) structures, the latter exhibiting, as is often the case, the best agreement with the experimental data. Nb5+ and Ta5+ cations having the same size, niobium and tantalum isotypes have usually very close cell parameters. However, those of NaNbO2F2 and NaTaO2F2, particularly c, differ in unusual proportions. This difference in c parameters is due to stronger second-order Jahn-Teller effect (SOJTE) for the cis-[NbO4F2]5– than for the cis-[TaO4F2]5– octahedra, further confirmed by band structure and projected density of states calculations. Furthermore, by optimizing the synthesis conditions of these compounds using thermal analysis, a very low amplitude endothermic event, upon heating, was observed only for NaNbO2F2. An extensive analysis of the variable temperature (VT) PXRD data revealed that this event is related to a deviation from linearity of the cell parameters evolution and that structural features of these two isotypes evolve differently with temperature.