Alligator juniper can be made into particleboard and is occasionally milled as lumber. The wood is also used to make furniture. It is most commonly used to make various novelty products such as bookends, lamp bases, or small chests.
Alligator juniper is an important component of the southern portion of pinyon-juniper woodlands.
Alligator juniper provides shade and shelter for wildlife and livestock. 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.