We assessed multiple environmental factors that might influence the population vitality of the epiphytic lichen Lobaria pulmonaria at the individual tree and habitat levels in partially overgrown wooded meadows in Estonia. A total of 301 trees of four species were sampled at nine study plots, using a stratified factorial scheme, 151 colonized by L. pulmonaria and 150 not colonized by L. pulmonaria forming the control group. We used the Generalized Linear Models (GLZ) to identify a complex of factors which predicts the probability of the lichen occurring on tree trunks and the presence of apothecia on its individuals. We employed the General Linear Mixed Model (GLMM) to study the relationship between cover of L. pulmonaria and environmental factors. The occurrence probability of L. pulmonaria on tree trunks increased with increasing light availability and height of deciduous shrubs near the trunk, and decreased with increasing distance to the nearest colonized tree. The host tree species and its trunk properties were also of importance, particularly the facilitating effect of the cover of bryophytes upon L. pulmonaria. The probability of occurrence of apothecia increased with maximum values of bark pH and cover of L. pulmonaria on the trunk. We conclude that partially overgrown wooded meadows are suitable habitats for L. pulmonaria. However, to maintain the vitality of these populations, a specific management scheme, preventing development of a dense stand, should be applied. Management requirements would include 1) selective cutting of overgrowing coniferous trees (particularly spruce), 2) preservation of adult and younger potential host trees within 10–20 m of colonized trees, 3) preservation of scattered deciduous shrubs in the vicinity of the host trees.