Wettability is a crucial factor controlling fluid transport and distribution in reservoir rocks. A significant discrepancy of reported contact angles for air plasma cleaned calcite-water-gas systems are evident from the literature. This work focuses on finding possible explanations for these discrepancies by studying the effect of two surface cleaning methods on the surface chemistry, which was utilized by employing XPS and TOF-SIMS analysis. Observed chemical changes were then discussed in relation to wettability. The two methods are i) air plasma cleaning, and ii) argon cluster ion cleaning. Air plasma cleaning exhibits a degree of reactivity towards the surface. The two surface cleaning methods are very similar in regard to efficiency. Air plasma cleaning of calcite surfaces resulted in an accumulation of low levels of metal oxides/hydroxyls. It was found that both quartz and calcite remain intact after surface cleaning, that is, neither of the cleaning processes degrade the material. It is suggested that the discrepancies in reported contact angle values is a combined effect of several factors, such as different degrees of i) surface roughness, ii) unavoidable adventitiously adsorbed hydrocarbons on the sample surfaces, and iii) non-native bulk components such as metal oxide/hydroxyls and biomarker material.