Cliffs are unique ecosystems with an outstanding but relatively unknown plant diversity, harboring rare, endemic and threatened species, but also rock-specialist or generalist species that can become locally common and dominant on cliffs. The rising popularity of climbing represents an increasing threat to cliff biota, affecting community composition and potentially diminishing diversity and species associations. We used a novel sampling design of closely-paired climbed versus unclimbed points along the cliff-face. We sampled along climbing routes of different climbing intensities in El Potrero Chico (Nuevo León, Mexico), identifying plant species and analyzing species associations and community composition in climbed and unclimbed plots. Diversity on the sampled cliffs was high, even greater than in other regional ecosystems. We found reduced abundance, cover, and diversity in climbed plots, irrespective of climbing intensity. Dominant species on the sampled cliffs were the most negatively affected by rock climbing in terms of abundance, and some locally rare species, including endemics and endangered species, were entirely absent from climbed plots. Co-occurrence analysis showed that the number of associations between pairs of dominant and common species were greatly reduced in climbed plots, and that positive associations between locally rare species existed in unclimbed plots but not in climbed plots, which may contribute to the disappearance of endemic and threatened species. Finally, NMDS analysis revealed that the community composition changed significantly due to climbing. Our results indicate that conservation science should convince stakeholders of the need for a holistic conservation of cliff ecosystems and not focus solely on emblematic or rare species, since plant community dynamics and preservation depend on interactions between plant species.