Migrant cave‐dwelling insectivores that rely on specific caves for maternity and hibernation, like the Natal long‐fingered bats Miniopterus natalensis in South Africa, may be at particular risk of population decline in an urbanising world. As a step towards the conservation of caves and cave‐dwelling bats in South Africa, this study aimed to (i) broadly identify the number of caves used by bats (any species) and specifically M. natalensis, throughout South Africa, (ii) investigate the number of maternity and hibernacula roosts currently known for M. natalensis, (iii) assess the number of caves located in formal protected areas, (iv) determine potential migration paths/corridors between hibernacula and maternity sites and (v) evaluate the potential threats (like onshore wind facilities) along potential migratory routes. A meta‐analysis of scientific literature and websites was conducted to identify caves throughout South Africa and locations of maternity and hibernacula roosts for M. natalensis. Roosts were assessed to determine whether (i) they were located in protected areas, (ii) they were used for eco‐tourism and (iii) the distance to primary roads and onshore wind energy facilities. Next, likely migratory paths were modelled between maternity and hibernacula sites using least‐cost path analysis and the threats along potential routes were investigated. A total of 92 caves were identified, 50 were reported to contain bats. M. natalensis were recorded in 37 caves, and of those, only 9% are currently located inside protected areas. A total of 12 least‐cost paths were modelled, and various paths intersected potential threat risk elements. Our analysis provides the first description of the potential migration corridors for M. natalensis in South Africa, as well as the current conservation status of bat‐inhabited caves. For a developing country set to experience increased urbanisation pressures, this study highlights the need for conservation measures for South African caves and the dependent bats.