Research highlights: shifts in the composition and functional diversity of lichen biota reflect changes in the environment caused by climate warming and eutrophication. Background and objectives: studies on lichen functional diversity and refinement in the functional traits of lichen biota under the pressure of changing environmental factors are currently of great scientific interest. The obtained results are interpreted in relation to specific habitat properties and their modifications due to the potential effects of climate change and atmospheric pollution. The aim of the work was to investigate changes in lichen species composition and functional diversity, as well as to identify factors responsible for them at different forest ecosystem scales. Materials and Methods: we identified factors responsible for changes in lichen biota in a unique Białowieża Forest ecosystem by analyzing shifts in species optima and functional diversity at the forest community, tree phorophyte, and substrate levels. We examined individual lichen species’ responses and temporal shifts in the species composition for each historical and resampled dataset using a community-weighted means of functional lichen traits and Wirth ecological indicator values. Results: the most evident change took place at the level of individual species, which shifted their realized optima: 25 species demonstrated a shift to co-occur with lichens of higher nitrogen demands, 15 demonstrated higher light demands, 14 demonstrated higher temperature preferences, and six demonstrated lower moisture preferences. At the level of forest communities, biota shifted towards the higher proportion of nitrogen-demanding and the lower proportion of moisture-demanding species. At the level of phorophyte species, biota changed towards an increased proportion of lichens of higher temperature preferences. For the substrate level, no directional shifts in lichen species composition were found. Conclusions: climate change has influenced lichen biota in Białowieża Forest, but the main driver of lichen species composition was found to be eutrophication. We suppose that other overlapping factors may contribute to biota shifts, e.g., the extinction and expansion of phorophyte tree species.