Abstract A key requirement for the correct interpretation of high-resolution X-ray spectra is that transition energies are known with high accuracy and precision. We investigate the K-shell features of $\mathrm {Ne}$ Ne , $\mathrm {CO}_2$ CO 2 , and $\mathrm {SF}_6$ SF 6 gases, by measuring their photo ion-yield spectra at the BESSY II synchrotron facility simultaneously with the 1s–np fluorescence emission of He-like ions produced in the Polar-X EBIT. Accurate ab initio calculations of transitions in these ions provide the basis of the calibration. While the $\mathrm {CO}_2$ CO 2 result agrees well with previous measurements, the $\mathrm {SF}_6$ SF 6 spectrum appears shifted by $∼ $ ∼ 0.5 eV, about twice the uncertainty of the earlier results. Our result for $\mathrm {Ne}$ Ne shows a large departure from earlier results, but may suffer from larger systematic effects than our other measurements. The molecular spectra agree well with our results of time-dependent density functional theory. We find that the statistical uncertainty allows calibrations in the desired range of 1–10 meV, however, systematic contributions still limit the uncertainty to ${∼ }$ ∼ 40–100 meV, mainly due to the temporal stability of the monochromator energy scale. Combining our absolute calibration technique with a relative energy calibration technique such as photoelectron energy spectroscopy will be necessary to realize its full potential of achieving uncertainties as low as 1–10 meV. Graphical abstract