The park's museum collection includes both cultural and natural history collections.
The cultural collections include: archeological materials systematically collected from within the park's boundaries and associated field reports; historic objects associated with the area's 19th and 20th century exploration, settlements and mining; archival and manuscript collections such as those associated with Robert Limbert; photographs; and scientific and resource management records. Cultural materials obtained from systematic surveys are housed at Idaho State University in Pocatello or in the park's museum storage facility along with items collected by Craters of the Moon staff over the years.
The natural history collections include: a herbarium of vascular and nonvascular plant species; geological specimens from throughout the park; some mammal and reptile specimens; and associated project documentation and reports.