The roots of many trees in temperate and boreal forests are sheathed with ectomycorrhizal fungi (EMF) that extend into the soil, forming intimate contact with soil minerals, from which they absorb nutrient elements required by the plants and, in return, are supported by the organic carbon photosynthesized by the trees. While EMF are strongly implicated in mineral weathering, their effects on mineral surfaces at the nanoscale are less documented. In the present study, we investigated the effects of symbiotic EMF on the topography of a chlorite mineral using atomic force microscopy. A cleaning protocol was successfully applied to remove fungal hyphae without altering the underlying mineral structure and topography. Examination of the exposed chlorite surface showed the presence of primary channels, of the order of a micron in width and up to 50 nm in depth, the morphology of which strongly indicates a fungal-induced origin. Smaller secondary channels were observed extending from the primary channels and would appear to be involved in their enlargement. The presence of channels is the first nanoscale demonstration of the effects of fungal interaction, fuelled by plant photosynthate, on the topography of a chlorite mineral, and it provides clear evidence of the ability of EMF to enhance mineral dissolution.