To determine whether globally increasing atmospheric carbon dioxide (CO2) concentrations can affect carbon partitioning between nonstructural and structural carbon pools in agroforestry plantations, Populus nigra was grown in ambient air (about 370 μmol mol−1 CO2) and in air with elevated CO2 concentrations (about 550 μmol mol−1 CO2) using free-air CO2 enrichment (FACE) technology. FACE was maintained for 5 years. After three growing seasons, the plantation was coppiced and one half of each experimental plot was fertilized with nitrogen. Carbon concentrations and stocks were measured in secondary sprouts in seasons of active growth and dormancy during 2 years after coppicing. Although FACE, N fertilization and season had significant tissue-specific effects on carbon partitioning to the fractions of structural carbon, soluble sugars and starch as well as to residual soluble carbon, the overall magnitude of these shifts was small. The major effect of FACE and N fertilization was on cell wall biomass production, resulting in about 30% increased above ground stocks of both mobile and immobile carbon pools compared with fertilized trees under ambient CO2. Relative C partitioning between mobile and immobile C pools was not significantly affected by FACE or N fertilization. These data demonstrate high metabolic flexibility of P. nigra to maintain C-homeostasis under changing environmental conditions and illustrate that nonstructural carbon compounds can be utilized more rapidly for structural growth under elevated atmospheric [CO2] in fertilized agroforestry systems. Thus, structural biomass production on abandoned agricultural land may contribute to achieving the goals of the Kyoto protocol.