We examined a study plot sampled in the Conecuh National Forest of southern Alabama in 1999 and again in 2016 after stand thinning and persistent prescribed fire were used to improve habitat quality. These management activities were designed, in part, to enhance habitat quality for the gopher tortoise (Gopherus polyphemus), a species considered for protection under the Endangered Species Act because of range-wide population declines. Comparisons of vegetation structure were made at burrows that were active in 1999 and remained active in 2016, and at burrows that were active in 1999 but were classified as abandoned in 2016. Burrows that remained active across this span of time were distinctive in retaining a greater reduction of canopy cover and lacking hardwoods while having a high percentage of longleaf pine in neighboring canopy trees. Active burrows that were abandoned in 2016 were distinctive in possessing hardwoods among neighboring canopy trees, lacking pine seedlings in the midstory, and having increased frequency of legumes and decreased bare ground in the understory. All burrows experienced a decrease in canopy cover and an increase in distance to, and dbh of, neighboring canopy trees; all burrows also had a decrease in litter and non-legume forbs as well as an increase in shrub stems in the understory and midstory. These results indicate that management activities were successful in opening canopy cover but were largely unsuccessful at reducing shrub stems and increasing understory grasses and forbs. Nevertheless, burrows of gopher tortoises increased in abundance during this time period. The size distribution of these burrows changed from a unimodal distribution dominated by adults to a bimodal distribution indicative of increased juvenile recruitment. Thus, the gopher tortoise population increased in association with vegetation changes that suggest tortoises are more sensitive to shading caused by canopy closure than they are to available forage.