The flora of the region consists of the tallgrass prairie association, upland hardwood association, bottomland hardwood association, and their transition zones. Since the forest area is located mainly on soils which formed under forest vegetation, plants of the prairie are not common. However, big bluestem, switch grass, Indian grass, prairie cordgrass, purple coneflower, round headed bush clover, lead plant, mountain mint, and various other native grasses and forbs do occur in open, non-forest areas. These non-forest areas are also managed in accordance with the Stephens State Forest Management Plan.
On the more productive upland sites, white oak, red oak, and hickory are common. The less fertile sites contain more black oak, bur oak, shingle oak, and hickory. The bottomland timber type includes red and white elm, cottonwood, hackberry, ash, silver maple, and black walnut.
Many areas around the forest had been planted to coniferous trees and non-native hardwoods. Many of these plantings were completed by the CCC in the early days of the forest or, more recently, by state forest staff for reforestation, research and demonstration. These plantings include a variety of pines, spruce, black locust, tulip poplar, and many others.