The pepper pot fungus is threatened by the disturbance of its habitat, such as the removal of certain trees or a decrease in grazing (5).
The pepper pot fungus is a candidate species for listing in Appendix I of the Convention on the Conservation of European Wildlife and Natural Habitats, otherwise known as the Bern Convention (3)(7). Recommendations for its conservation include the use of traditional farming methods on sites containing this fungus and the prevention of clear felling (5).