Transition metal-based sodium fluoro-perovskite of general formula NaMF3 (M = Fe, Mn, and Co) were investigated as cathode materials for rechargeable Na-ion batteries. Preliminary results indicated Na-ion reversible intercalation but highlighted the need to find optimization strategies to improve conductivity and to modulate the operating voltages within experimentally accessible electrolytes’ stability windows, in order to fully exploit their potential as high-voltage cathodes. In this study, we combined experimental and computational techniques to investigate structures, defects, and intercalation properties of the NaFe1-xMnxF3 and NaCo1-xMnxF3 systems. Through the use of a simple solvothermal synthesis, we demonstrated the possibility to modulate the sample’s morphology in order to obtain fine and dispersed powder samples. The structural results indicated the formations of two solid solutions with a perovskite structure over the entire compositional range investigated. Atomistic simulations suggested that Na-ion diffusion in these systems was characterized by relatively high migration barriers and it was likely to follow three-dimensional paths, thus limiting the effect of anti-site defects. The correlation between structural and computational data highlighted the possibility to modulate both ionic and electronic conductivity as a function of the composition.