Wooded meadows with a history of traditional land use over thousands of years support a great diversity of various taxa. Today, however, high-species-rich communities in wooded meadows are threatened because of the cessation of traditional management in large areas. We studied lichen communities on 136 deciduous trees (Betula spp., Fraxinus excelsior and Quercus robur) in 12 wooded meadows in three regions of Estonia, and assessed the effect of habitat change due to the abandonment of traditional management on epiphytic lichen species composition, considering factors on three spatial scales: regional, habitat and individual tree. The variation partitioning approach in partial Canonical Correspondence Analysis (pCCA) revealed that most of the variation in species composition is described by the species of host tree and tree bark pH. Other tree level variables, foremost tree diameter, described as much of the compositional variation as geographic location (region) or environmental conditions in wooded meadows. Of the environmental factors studied, woodland canopy cover is the strongest predictor of the change in epiphytic lichen species composition from the community type of semi-open wooded meadows to species-poor communities characteristic of secondary forest. General Linear Model (GLM) analysis of the abundance of the 35 most frequently observed lichen species revealed that more than half of them (21) are influenced by site openness (canopy cover and/or undergrowth density), showing that increasing canopy cover has a negative effect on the abundance of epiphytic lichen species characteristic of traditionally managed semi-open wooded meadows. The results emphasize that the preservation of large old deciduous trees of various species and the maintenance of the semi-open structure of stands are vitally important for the protection of epiphytic lichen communities in wooded meadows.