The linkage between above-ground biomass production and below-ground carbon fluxes as influenced by silviculture has been insufficiently studied. We tested the effects of stocking, clone, fertilization, and follow-up herbicide treatments on below-ground carbon flux (BCF), above-ground biomass production (AGB), the ratio (BCF/AGB), tree diameter (DBH), height (H), basal area (G), and leaf area index (LAI) for a Pinus radiata D. Don plantation trial in the Canterbury region of New Zealand. Mixed-effects analysis of variance was carried out using data at the plot and clone levels. The H, DBH, G, AGB, BCF and the BCF/AGB ratio were influenced significantly by the main effects of stocking (p < .05), and the follow-up herbicide (p < .001). The main effects of clone had significant influence on H (p < .001), BCF (p < .01) and the BCF/AGB ratio (p < .01). Values of AGB and G increased with stand density, while DBH and H decreased with stand density. The significant stocking × follow-up herbicide interactions observed for DBH, G and AGB, suggested that follow-up weed control alleviated understory-induced water and nutrient stresses. Significant clone × follow-up herbicide interactions for DBH and AGB (p < .05), and clone × stocking interactions for G (p < .05), and no interaction of silvicultural treatments for BCF and BCF/AGB ratio were observed. Clones 1 and 3 exhibited greater AGB and smaller BCF/AGB ratio, compared to slower growing clones (i.e., Clones 4 and 5), suggesting certain clones were more productive above-ground at the expense of less carbon partitioned below-ground. These findings highlight that stocking, follow-up herbicide, and clone, in that order, had the greatest influence on above- and below-ground variables, suggesting that those silvicultural practices shifted carbon partitioning above-and below-ground. We conclude that well-performing clone planted with appropriate stand density and with follow-up weed control treatments may increase aboveground radiata pine productivity.