The forested slopes of Capulin Volcano are covered in pinyon/juniper woodland. This short-statured forest is dominated by pinyon pine, juniper, sumac, wavyleaf oak, Gambel’s oak, and mountain mahogany. These trees are swarmed by lady beetles in the summer, provide protective cover for birds and small mammals, and are a key food source for deer. Scattered throughout the monument are ponderosa pine and a small stands of aspen.

Pinyon pine is found throughout the monument, from the slopes of the volcano to the base and surrounding area. The monument's high elevation and low annual precipitation create a well-suited habitat for the pinyons that thrive in arid conditions. The pinyon serves the volcano in providing a sturdy root base that slows the steep slopes' rate of erosion. For wildlife, the trees' seeds are an important food source for birds, squirrels, deer, and even bear. Native Americans also utilized the seeds in their diet, and the tree's sap for basket and jewlrey making. As the state tree of New Mexico, the pinyon has and continues to be a sustenance-providing and iconic part of life in the southwest.

Juniper grows alongside the pinyon pine at Capulin Volcano. Two species exist within the monument, the one-seed juniper (Juniperus monosperma) and the Rocky Mountain juniper (Juniperus scopulorum). Junipers have tight, scaly leaves that are compact to the branch and bark that has a shredded appearance. The juniper berry, light blue and pea-sized, is actually the plant's cone, and has been known to be used as a flavoring for cooking and tea. Junipers can grow up to 40 feet high, but growth is very slow and depends on the amount of water and nutrients available. The resiliency of the juniper is shown in especially dry, sloping land; the gnarled and twisted shape of the tree is a result of too little water.

Ponderosa pines are found scattered throughout the monument. These large pines usually occur in mountains in pure stands. They are more solitary and mixed through the other woodlands in the lower elevations of Capulin Volcano. Stand close and take a smell - many large ponderosas are said to smell like vanilla or butterscotch.

A grove of Aspen trees light up the base of the volcano each fall as the leaves turn a yellowish orange.