Forest logging can be detrimental for non-vascular epiphytes, determining the loss of key components for ecosystem functioning. Legal logging in a Mediterranean mixed oak forest (Tuscany, Central Italy) in 2016 heavily impacted sensitive non-vascular epiphytes, including a large population of the threatened forest lichen Lobaria pulmonaria (L.) Hoffm. This event offered the background for this experiment, where the potential effects of logging in oak forests are simulated by means of L. pulmonaria micro-transplants (thallus fragments <1 cm). Our working hypothesis is that forest logging could negatively influence the growth of the thalli exposed in logged stands compared to those exposed in unlogged stands. One hundred meristematic lobes and 100 non-meristematic fragments are exposed for one year on 20 Turkey oak trees (Quercus cerris), half in a logged and half in an unlogged stand. Chlorophyll (Chl) a fluorescence emission and total chlorophyll content are used as a proxy for the overall vitality of the transplants, while their growth is considered an indicator of long-term effects. Generally, vitality and growth of the transplants in the logged stand are lower than in the unlogged stand. Both vitality and growth vary between the meristematic and non-meristematic fragments, the former performing much better. Hence, irrespective of forest management, meristematic fragments show higher growth rates (0.16–0.18 cm2 year−1) than non-meristematic ones (0.02–0.06 cm2 year−1). Considering that a conservation-oriented management for this species should be tailored at the habitat-level and, especially, at the tree-level, our results suggest that for appropriate conservation strategies, it is necessary to consider the life cycle of the lichen, since the probability of survival of the species may vary, with meristematic fragments having more chance to survive after logging.