Several recent studies have shown that some skeletal limestone reservoirs are far more oil-wet than the typical, water wet, biogenic, limestone reservoirs, such as chalk. It is challenging, even with state-of-the-art approaches, to completely remove the residual hydrocarbons from skeletal limestone core samples and restore the pore surfaces to the water wet conditions that are assumed to prevail before oil entered from the source rock. We used a combination of gas chromatography mass spectrometry, X-ray photoelectron spectroscopy, and time-of-flight secondary ion mass spectrometry to investigate pore surface composition and we propose an explanation for the phenomena. The hydrophobic nature of pore surfaces is likely caused by adsorbed organic molecules that are strongly attached to the calcite surfaces through carboxylic functional groups and their fatty ends serve as anchors for the lipophilic oil components. The strong binding of the carboxylate to the pore surfaces explains why it is only possible to remove some of the organic material using the conventional core cleaning methods, such as Soxhlet solvent extraction. Unless a solvent is able to replace the carboxylate terminated species, the rock remains oil-wet or at least mixed wet, regardless of the type or extent of the cleaning procedure.