In the North Central Coast of Vietnam, vegetation loss due to war and overuse has been severe. In degraded coastal sand dune forest ecosystems, land managers often plant exotic species like Acacia spp. to reduce sand dispersal and increase forest cover. However, the impacts that Acacia plantations have on the ecological functions of these forests have not been fully demonstrated. To estimate the long-term impacts of Acacia plantations on revegetation in sand dune areas, we investigated the understory vegetation (height < 130 cm) in a total of 54 quadrates (1 m × 1 m), including nine natural forests and nine plantations. We identified 956 individuals, with 797 found in natural forests and 159 in plantations. The species found in the understory vegetation in natural forests were well-distributed among vines, trees, and herbs. In contrast species found in plantations were predominantly herbs. We compared four diversity indices (richness, Shannon, evenness, and Menhinick) between the plantations and natural forests and found that all were significantly higher in natural forests (P < 0.05). The NMDS analysis, PERMDISP, and PERMANOVA confirmed significant differences in the understory vegetation structure between natural forests and plantations. Among the measured environmental factors, we observed a significant difference only in soil pH between the two forest types, and all measured environmental factors did not have a statistically significant impact on ecosystem function that could explain the variation of understory vegetation structure. These results underscore the critical role of natural forests in restoring and supporting the long-term development of coastal sand dune ecosystems in North Central Vietnam.