<p>Lichens contribute to increasing biodiversity in forests and have a substantial impact on forest dynamics, including water cycling and microclimate shaping. Natural disturbances, ongoing climate change, forestry practices, and habitat fragmentation disrupt the structural complexity of the woodland landscape, posing a serious threat to sensitive stenoecious species. Long-term studies on the acclimation abilities and physiological response of lichens to altered microclimatic conditions at the local landscape scale are largely lacking. We transplanted thalli of three epiphytic lichens confined to forest habitats to varying degrees from the forest interior to its edge for three growing seasons. After each season, we monitored basic physiological traits related to photobiont photosynthesis and mycobiont activity in both habitat types. Weather variables were continuously recorded to precisely define differences between habitats in terms of microclimatic conditions. Large diurnal fluctuations in climatic variables cause lichens at the forest edge to function under a different metabolic activity regime. Ecophysiological acclimation abilities varied among the studied lichens and we observed species-specific responses to relocation, in general: <i>Cetrelia cetrarioides</i> showed low resistance to changes in habitat conditions and climatic stress, <i>Lobaria pulmonaria</i>—intermediate resistance, and <i>Flavoparmelia caperata</i>—relative insensitivity. We consider determining the concentrations of TBARS (thiobarbituric acid reactive substances) in lichens a promising assay for the early identification of adverse climatic changes in forest habitats. The successful adaptation of forest lichens to forest edge conditions is influenced by functional traits of a given lichen and the pattern of short-time scale climatic fluctuations.</p>