This species is only found on Floreana (Charles) Island at elevations above 250m in moist highland forest habitat. Prime breeding habitat is dominated by Scalesia pedunculata trees. It is threatened by habitat loss which has occurred through clearance for agriculture and introduced predators such as rats, mice, cats, and the smooth-billed ani. The diurnal Galapagos short-eared owl is its only remaining natural predator. The introduced parasite Philornis downsi is a significant threat to the survival of this species. Parasitic larvae of this fly suck blood from nestlings and cause considerable mortality.
The range of beak sizes of C. pauper on Floreana and Camarhynchus psittacula on Isabela is roughly the same. This reflects the fact that the two species feed on the same type and size of insect. The beak of the Medium Tree Finch is intermediate in size between the Small Tree Finch and Large Tree Finch. All three species are found in the same habitat.