Environmental control strategies are commonly practised to limit biodeterioration issues threatening indoor cultural heritage objects, while they are still poorly exploited for the conservation of outdoor stone heritage surfaces, including rock art. In this study, we evaluated the environmental factors driving the diversity and abundance of lithobiontic communities in the Rock Engravings National Park of Naquane (UNESCO WHS n. 94, Italy). The survey considered 23 rocks that had been cleaned in the last three (3YC) or twelve (12YC) years or more than 40 years ago (NRC). A cyanobacteria-dominated biofilm and lichens (37 taxa) were the most widespread and abundant lithobiontic components, prevailing on 3YC–12YC and NRC rocks, respectively. On the latter, a turnover of xerophytic and meso-hygrophytic lichen communities was observed. On 3YC–12YC rocks lichen colonization, if present, was limited to nitrophytic species, including common epiphytes from surrounding trees and a small number of meso-hygrophytic species, with a prevalence of asexual reproductive strategies. Multivariate analyses including environmental parameters (canonical correspondence analyses) indicated that tree cover and the presence of bare or vegetated ground upstream of the rocks, probably prolonging wetness and providing nutrients by water transport, are the factors mostly related to the microbial and lichen recolonization of 3YC–12YC surfaces. On this basis, an experiment on preventive conservation was conducted, consisting of a new cleaning of a strongly recolonized 3YC surface combined with the building of a small wall to protect part of the rock from prolonged water fluxes. The fluorimetric and colorimetric monitoring of the rock surface, carried out 40 months after this new cleaning intervention, displayed recolonization on the unprotected area only, indicating the potential of preventive conservation strategies in outdoor environments.