Although examples are rare, conflicts between species of conservation concern can result from habitat restoration that modifies habitat to benefit a single taxon. A forest restoration program designed to enhance habitat for endangered red-cockaded woodpeckers (Picoides borealis) may be reducing available habitat for the eastern spotted skunk (Spilogale putorius), a forest-adapted sympatric species of conservation concern that occurs in the Ouachita National Forest, Arkansas, U.S.A. At small scales, eastern spotted skunks select early successional forest with structural diversity, whereas red-cockaded woodpeckers prefer mature pine (Pinus spp.) habitat. We surveyed for eastern spotted skunks at 50 managed forest stands, modeled occupancy as a function of landscape-level habitat factors to examine how features of restoration practices influenced occurrence, and compared known occupied forest stands to those where active red-cockaded woodpecker nesting clusters were located. The most-supported occupancy models contained forest stand age (negatively associated) and size (positively associated); suggesting eastern spotted skunks primarily occupy large patches of habitat with dense understory and overhead cover. Red-cockaded woodpecker nesting clusters were located in smaller and older forest stands. These results suggest that increased overhead cover, which can reduce risk of avian predation, enhances occupancy by small forest carnivores such as eastern spotted skunks. Management activities that increase forest stand rotation length reduce the availability of young dense forest. The practice may enhance the value of habitat for red-cockaded woodpeckers, but may reduce the occurrence of eastern spotted skunks. Implementing plans that consider critical habitat and extinction risks for multiple species may reduce such conservation conflict.