Carbon (C) flux and partitioning responses of Pinus radiata (D. Don) clones to a factorial combination of nitrogen (N) and phosphorus (P) supply were estimated in small trees growing in a greenhouse over 44 weeks. Our objective was to use a C budget approach at the plant level to examine how a factorial combination of N and P additions and genotype modify gross primary production (GPP), net primary production (NPP), absolute C fluxes apportioned to aboveground net primary production (ANPP), aboveground plant respiration (APR), total belowground carbon flux (TBCF) and the partitioning of GPP to ANPP, APR and TBCF. Single N or P additions increased plant NPP and GPP similarly, but their combined effects exceeded those of their individual contributions. Nitrogen and to a lesser extent P additions enhanced carbon-use efficiency (CUE, NPP:GPP) and C partitioning to ANPP at the expense of TBCF. The fraction of GPP partitioned to APR was invariant to N or P additions. The ratio of soil respiration (FS) to TBCF was significantly greater in the low-N low-P addition treatment (61%) than in those treatments with single or combined N and P additions (49%). The slowest growing clone partitioned a significantly smaller fraction of GPP to ANPP (29%) than one of the faster-growing genotypes (33%). This research provides insight into how N and P regulate the C fluxes and partitioning in individual plants. Our results contribute to explaining clonal variation in aboveground growth rates and suggest that greater gains in CUE and partitioning to ANPP occur with addition of N rather than P supply.