Geophagy, the deliberate ingestion of soil, is a widespread practice among animals, including humans. Although some cases are well documented, motivations and consequences of this practice on the health status of the consumer remain unclear. In this paper, we focused our study on chimpanzees (Pan troglodytes schweinfurthii) of the Kibale National Park, Uganda, after observing they sometimes ingest soil shortly before or after consuming some plant parts such as leaves of Trichilia rubescens, which have in vitro anti-malarial properties. Chemical and mineralogical analyses of soil eaten by chimpanzees and soil used by the local healer to treat diarrhoea revealed similar composition, the clay mineralogy being dominated by kaolinite. We modelled the interaction between samples of the two types of soil and the leaves of T. rubescens in gastric and intestinal compartments and assayed the anti-malarial properties of these solutions. Results obtained for both soil samples are similar and support the hypothesis that soil enhances the pharmacological properties of the bio-available gastric fraction. The adaptive function of geophagy is likely to be multi-factorial. Nevertheless, the medical literature and most of occidental people usually consider geophagy in humans as an aberrant behaviour, symptomatic of metabolic dysfunction. Our results provide a new evidence to view geophagy as a practice for maintaining health, explaining its persistence through evolution.