Naturally regenerated pine ecosystems cover 11.7 Mha of the southeastern United States, comprising 13.8% of the forested land, and represent an important component in the carbon balance for the region. These forests are exposed to strong climatic variability from extreme multiyear droughts to above average precipitation years, many are actively managed with prescribed fire and some modification of tree density by cutting. This study is unique in assessing the effects of management and climatic variability for two decades on the carbon (C) dynamics and long-term net ecosystem C balance (NECB) for an actively-managed naturally regenerated pine ecosystem. We used 21 years of eddy covariance estimates of net ecosystem C production (NEP), combined with periodic tree inventories, understory biomass and forest floor assessments. Forest management included six prescribed fire cycles on a three-year rotation beginning in the third year of the study, and a preparatory cut which reduced basal area by 20% from 17.05 ± 0.66 m2/ha during the spring of 2016. The mean annual NEP was 3.32 ± 1.37 Mg C/ha yr−1, with a range of 5.35 Mg C/ha (1.30 to 6.65 Mg C ha/yr), was not significantly affected by fire and was mainly controlled by water availability. A combination of aboveground C assessments (tree and understory) and NEP indicates that C stored belowground accounted for 23% of NEP, with part of this used to support aboveground understory growth after fire. Net ecosystem carbon balance (NECB, integrated NEP and C losses from management) fluctuated in a range of 15.5 Mg Cha−1 (6.7 to −8.8 Mg C ha -1) and was sensitive to management. However, a higher NECB during the second decade than in the first (15.3 Mg C/ha vs. 2.7 Mg C/ha) reflected increased NEP (40 Mg C/ha vs. 25.4 Mg C/ha) as it responded to a greater water availability, despite similar amounts of C lost from management activities during both decades. At the end of the 21 years study, the ecosystem had incorporated 22.6 Mg C ha -1, indicating that actively managed naturally regenerated pine ecosystems in the region can mitigate C dioxide emissions under a broad range of climatic conditions, reduce wildfire risks, while providing numerous ecosystem services.