Research indicates that the mean volatile oil content of alligator juniper is less than that of either Rocky Mountain or Utah juniper. In the Dos Cabezos Mountains of southeastern Arizona, alligator juniper is reported to be one of the seven most important foods of both mule deer and white-tailed deer. The foliage of alligator juniper relatively unpalatable to livestock and most wild ungulates. Little specific information exists on the food value of alligator juniper. Alligator junipers provide hiding and thermal cover and migration corridors for a variety of animals.
Young trees provide cover for elk, deer, and small mammals.
Wood extractives of alligator juniper may be of value although the precise characteristics of the extractives of this species are poorly known. Juniper wood is associated with traditional values in a number of Native American cultures. The Zuni used alligator juniper cone-berries to flavor foods such as cornbread and blood sausage. Pinyon-juniper woodlands have been increasing in extent since settlement times. However, overgrazing offers another possible explanation.