The determination of the oxidation state and structural role of transition metals in minerals is a crucial challenge. XPS has proven to have a great potential in probing the site distribution and chemical states of Fe and Ti transition elements, provided that the right method to process the spectra is used. XPS spectra of these elements have the 2p core level region usually rich of features but the choice of the method for background removing can seriously affect the results of the quantitative analysis. Single crystals of brookite (TiO2) and natural micas (phlogopites) are investigated to examine the effect of background subtraction on Ti2p and Fe2p signals. The backgrounds used are: the “Linear” background; the traditional “Shirley” background; three different Tougaard-like backgrounds; and the more recent “shape parameter, κ” method. In the case of the studied natural micas, the Fe chemical state proportion (Fe2+/Fetot) obtained with the corrected spectra varies by 10%. It is shown that TiO2 oxides are not suitable as standard for octahedral Ti4+ signal in the studied micas. The “shape parameter, κ” method proves to provide supplementary information useful for a full interpretation of XPS signals.