Porous materials derived from natural resources, such as Luffa sponges, pomelo peel and jute fibres, have recently emerged as oil adsorbents for water purification, due to their suitability, low environmental impact, biodegradability and low cost. Here we show, for the first time, that the porosity of the fruiting body of polypore mushrooms can be used to absorb oils and organic solvents while repelling water. We engineered the surface properties of Ganoderma applanatum fungi, of which the fruiting body consists of a regular array of long capillaries embedded in a fibrous matrix, with paraffin wax, octadecyltrichlorosilane (OTS) and trichloro(1H,1H,2H,2H-perfluorooctyl)silane. Morphological and wettability analyses of the modified fungus revealed that the OTS treatment was effective in preserving the 3D porosity of the natural material, inducing super-hydrophobicity (water contact angle higher than 150°) and improving oil sorption capacity (1.8–3.1 g/g). The treated fungus was also inserted into fluidic networks as a filtration element, and its ability to separate water from chloroform was demonstrated.