The lesser horseshoe bat, Rhinolophus hipposideros, is the only member of its family found in Ireland. It is small, weighing roughly five to nine grams, with a body about the size of a human thumb. The most recent Irish population estimate places it at 12,870 individuals, scattered across only six counties in the west of Ireland in fragmented colonies of varying size. In the 2017 European Union assessment, the species' conservation status was recorded as unfavourable inadequate. The bats are vulnerable to habitat loss and to disturbance at their roosts. They are also extremely sensitive to artificial lighting; bats will abandon a roost if lighting increases near their site or along their foraging routes. The Ballymaglancy cave was recognised as a habitat for these bats at least as early as 1993. It was proposed as a Site of Community Importance in 2002 and formally designated a Special Area of Conservation in 2016.

In addition to the main cave, the Ballymaglancy Resurgence cave has been mapped: 417 metres in length, five metres in height, with about 50 metres unsurveyed as of 2015. The entrance lies in Galway, but most of the cave system extends underneath County Mayo, which has the strange consequence that some of County Mayo's geology can only be reached by entering County Galway. The sections of the cave carry names that read like a horror story: Wet Ear Passage, Mud Chamber, Boulder Chamber. The roof is low, so the approach requires crawling. The cave is prone to flooding. Inside, where the bats are not, the limestone has been shaped by water into gour pools and flowstone walls, calcite formations laid down drop by drop over thousands of years. The same water that creates this beauty also makes the cave dangerous to enter without expertise.

Conservation targets for the site set a minimum of 50 bats to be maintained or improved at Ballymaglancy. The current qualified mean of 28 bats, calculated from winter counts between 2013 and 2017, falls short of that target. Bat Conservation Ireland, the National Parks and Wildlife Service, and the Vincent Wildlife Trust share responsibility for monitoring. Summer roosts get one kind of attention, winter hibernacula another. The objectives include no decline in the quality of the winter roost, no decline in foraging area for 2.5 kilometres around the site, and no increase in artificial lighting within that radius. The bats winter here. They emerge in spring. The lights of the village must stay where they are.

The cave complexes around Cong, of which Ballymaglancy is one, were preserved in nineteenth-century Irish traditional music as well as in stone. The Irish air called The Caves of Cong, also known as Bean an Fhir Ruadh or The Red Haired Man's Wife, appears in the Collection of Irish Airs, Marches and Dances, Volume 1, of 1927, edited by Francis Murphy. The score is held at the Irish Traditional Music Archive. The tune travels with the caves, a reminder that long before designations and statutory instruments, the people of this stretch of limestone country knew exactly where the water disappeared into the rock and where it came back out again. The bats they may not have known were there. The caves they always did.