The crystal structure of the disordered modification of Ba7F12Cl2 has been carefully re-examined on several new crystals prepared under different conditions of synthesis. All single crystal structure refinements reveal a residual electron density of 3 e-/Å3 in the 0,0,0 position which is explained by the introduction of a small amount of sodium ions in the crystal. The title compound transforms from a disordered to an ordered modification at 800 °C. New structural data show a change in space group from P63/m to P6. During this process, a slight chemical change and the formation of nano-channels in the crystals is observed by electron microscopy. These changes were further studied by electron microprobe analysis, by spectroscopic methods and thermal analysis.