The impact of lichens on the conservation of monuments, such as the World Heritage Site (WHS) of Cappadocian churches, presents a multifaceted challenge for conservators. Previous studies have shown that lichens can both induce deterioration processes of stone through their penetration into the substrate and chemical interactions as well as provide bioprotection, forming encrustations including calcium oxalate layers, which help mitigating the effects of weathering, reducing water penetration and eolian erosion. Evaluating the impact of lichens requires a comprehensive understanding of various factors, which include the type of rock substrate, the colonizing lichen species, the monument architecture, and the prevailing physic-chemical weathering processes. This study aims to provide a comprehensive analysis of the impact of lichen colonization on Saint Simeon Church in the Paşabağı Valley (Turkey) with a multidisciplinary approach to investigate the interplay between lichens, microclimatic conditions, and the degradation of stone. Specifically, this study examines the influence of wind-driven rain (WDR) occurrences on lichen distribution and stone weathering to develop comprehensive conservation strategies. The results confirmed the previous observations and showed a prevalence of the protective role of lichens over their deterioration. The northwest side of the church, despite being heavily impacted by environmental factors such as WDR and freezing–thawing cycles, showed reduced deterioration due to extensive lichen coverage. In contrast, the northeast side, with lower lichen colonization, demonstrated more severe deterioration. These findings suggest that integrating the protective aspects of lichen colonization into conservation strategies can enhance their preservation.