Peru is among South America's most diverse countries with an astounding natural and cultural heritage that the country has a legal obligation to preserve. It is among the 17 most megadiverse places on earth. For centuries indigenous people have shaped Peru's cultural landscape, land use practices largely compatible with preserving biodiversity. In the modern, industrial era ecosystems and their unique species assemblages are, however, increasingly threatened. Cultural heritage sites have become important refugia for biodiversity. World-famous monuments such as Machu Picchu and lesser known sites (Tipón, Raqchi, Saqsaywaman, Ollantaytambo, Tarawasi, Qoricancha, etc.) are not only cultural heritage of humanity, they are equally important for the conservation of biodiversity. Tourists visiting these places will often be unaware that monuments are important secondary habitat for saxicolous lichens. Some may even consider lichens growing on these monuments aesthetically displeasing. Archaeologists are more worried, however, about the damage that these organisms may cause. Yet, although saxicolous lichens deteriorate their substrates, some species may also persist for centuries. Time scales at which lichen communities disintegrate, their substrates thus eroding, remain largely unknown. Strategies to clean surfaces are not necessarily effective. Frequent cleaning may accelerate erosion, with common species repeatedly re-invading, and more sensitive species disappearing. Mitigating biodeterioration, while preserving biodiversity, is not necessarily mutually exclusive. But, to develop strategies that achieve this goal, it is necessary to closely monitor the lichen communities dynamics at the sites. Here we propose using a combination of different archaeological, biological, and geological techniques to investigate how population dynamics of saxicolous lichens at different cultural heritage sites in Peru affect deterioration in the long-term: (1) photogrammetric monitoring, (2) establishing a reference collection, (3) investigate mineralogical changes (X-ray diffractometry), mineral cohesion (IR-spectroscopy), and organic matter content (CNH-analysis), and (4) microscopic analysis of the lichen substrate-interactions (reflected light microscopy, SEM).