This review elucidates current knowledge on the significant role of fungi and lichens in the biodeterioration of stone monuments. The effect caused by many epilithic lichen species in the deterioration of different types of stone has been extensively investigated and demonstrated. Nonetheless, many aspects of the deterioration mechanisms of microcolonial fungi (MFC) and endolithic lichens are still to be proved. An interesting hypothesis has recently been put forward involving the secretion of siderophores like compounds. Lichens can provide bioprotection for stone surfaces, acting as a barrier against weathering, retaining moisture, increasing waterproofing, reducing thermal stress and erosion, and absorbing pollutants. Nevertheless, the evaluation of biodeterioration vs. bioprotection cannot be generalised, since it can vary according to the behaviour of different species, as well as being affected by both the lithotype and the environment. In addition to the laboratory studies, more field studies of biological communities are required, to analyse their establishment and succession in natural conditions and after conservation treatments. In order to guarantee the best decision for stone conservation, cleaning operations should not be based on a generalised approach, but should rather be based on a careful evaluation of different aspects concerning biodeterioration and bioprotection.