Rhinolophus mehelyii roosts year-round in caves and mines and only rarely in other artificial underground sites (Puechmaille 2020). The species forages in the forest, but also frequently in semi-open habitats, whereas open habitats are avoided or preferred in different populations, and foraging sites are preferentially close to water (reviewed in Puechmaille 2020). Overall, habitat selection probably implies a combination of habitat features, food availability, and competition avoidance with R. euryale where these species are sympatric (Puechmaille 2020). The diet is largely dominated by moths but locally other prey types may also occur (Puechmaille 2020). Rhinolophus mehelyi only shows regional movements < 100 km, mostly between maternity, mating and hibernation sites (Hutterer et al. 2005).

In Europe, Rhinolophus mehelyi is patchily distributed in the southern part of the continent, through most of the Mediterranean region (Portugal, Spain, Italy, Albania, North Macedonia, Serbia, Greece, and Bulgaria, east to the western coasts of the Black Sea. It is considered possibly extinct in France (not mapped) and Romania. It also occurs in the Spanish territory of Ceuta, North Africa (López-Baucells et al. 2012). The range of altitudes where this species can be found varies between 0 and 2,000 m asl.

Outside Europe, the species occurs in Asia Minor, the Caucasus, Iran (eastern distribution limit) and south to northern Egypt, Cyrenaica (Libya), and the Maghreb (Tunisia, Algeria, and Morocco (Puechmaille 2020).

Rhinolophus mehelyi is protected by national legislation in most range states. There are also international legal obligations for its protection through the Eurobats Agreement and Bern Convention where they apply. It is included in Annexes II and IV of 92/43/EEC Habitats Directive and hence requires special measures for conservation including the designation of Special Areas for Conservation. To date, the species is protected in 234 Natura 2000 Sites but has already disappeared in some of them (Puechmaille 2020). The EU-LIFE project LIFE00 NAT/E/007337 in the Community of Valencia targets the protection of several bat species including the now tiny (70 individuals) population of R. mehelyi that occurs there, and the GRECABAT LIFE project (LIFE17 NAT/GR/000522) also included conservation actions for this species (Puechmaille 2020).

To preserve this species, it is essential to protect its cave habitats, as well as to conserve its foraging sites and avoid using pesticides and artificial lighting. Further research is necessary to understand the ecology of this species and identify management priorities for its habitat. Monitoring populations across the species' range is also highly important to track demographic trends and take appropriate conservation measures when necessary.