Apart from its historical importance, San Juan de la Peña is an ecological site of great value. It includes thick and varied wooded areas in an excellent state of conservation composed of Pinus sylvestris, beeches and lindens. This natural site has remained a virgin territory thanks to the conservationist policy practised by the monks for centuries. The huge masses of conglomerated rocks rise up to 1,000 and 1,290 metres, below which is the old monastery. They serve as places of nidification for an important colony of birds of prey.

This wild area stretches along 264 h occupied by Pinus sylvestris, in the high parts, and firs, oaks, holm oaks, holly trees, junipers, boxes and Arctostaphylos uva-ursi on the North slope. The Mediterranean microclimate produces a broad variety of plant species accompanied by characteristic flowers such as primroses, violets, hepatica and columbine flowers, as well as heathers and whortleberry bushes. On the cliff faces of San Juan de la Peña live birds of prey including lammergeyers, vultures and Egyptian vultures. The woods are home to badgers, wild boars, partridges and rabbits.