The holotype was collected by a local from an unknown location, thus its habitat is unknown (T. Doherty-Bone pers. comm. October 2012). Assuming it occupies habitats similar to other caecilians, possible habitats for this soil-dwelling species include both montane and lowland forest, fruit tree plantations, rural small-scale gardens and secondary forest. However, there is no information on the ecological preferences of this species and its breeding biology is also unknown (although it is suspected to be oviparous with direct development).

This species is known only from its holotype which is believed to have been collected near Limbe on the coast of south-western Cameroon. However, caecilians of the genus Crotaphatrema have only been found at high elevations, suggesting that Crotaphatrema bornmuelleri is also a high-altitude species and should be found on Mount Cameroon, which is the nearest mountain to Limbe (Lawson 2000 and Doherty-Bone et al. 2011) and may occur more widely.

It is not known from any protected areas and, in view of extensive past deforestation, its habitat in Limbe could require protection. Should the species be found at higher elevations, such as on nearby Mount Cameroon, it could occur within Mount Cameroon National Park (T. Doherty-Bone pers. comm. October 2012). Research is needed on its population status, natural history and threats.