Soil carbon sequestration is a crucial strategy for addressing climate change; however, the contribution of fast-growing tree plantations under drought conditions remains poorly understood. This study assessed the total belowground carbon flux (TBCF) of eight Eucalyptus genotypes over three years (ages 7–9) under two contrasting irrigation regimes in a plantation located in the Mediterranean region of Chile. The analysis included E. globulus, E. nitens × globulus (high- and low-yielding), E. nitens, E. badjensis, E. smithii, and E. camaldulensis × globulus, evaluated under irrigation (>75% field capacity) and drought (~25% above the permanent wilting point). The TBCF was estimated annually using a carbon mass balance approach, and productivity was assessed via the current annual increment (CAI). The results showed an average CAI of 27.4 m³·ha⁻¹·yr⁻¹ and a TBCF of 1204 gC·m⁻²·yr⁻¹ under irrigation, while under drought, the CAI was reduced by 24% and the TBCF by 13% (to 17.5 m³·ha⁻¹·yr⁻¹ and 1036 gC·m⁻²·yr⁻¹, respectively). E. smithii and E. nitens × globulus (high-yield) showed high stability, with CAI variations <10% and TBCF reductions <5%. In contrast, E. globulus and E. nitens×globulus (low-yield) exhibited >35% reductions in CAI and >20% in TBCF. A logarithmic relationship was observed between CAI and TBCF (R² > 0.80), with steeper slopes under drought, indicating increased belowground carbon allocation per unit of growth as the TBCF:CAI ratio increased from 44.0 under irrigation to 59.2 under drought, reflecting a shift in allocation strategy. These results suggest that under water-limited conditions, trees prioritize belowground functions (e.g., root activity and rhizosphere support), potentially at the expense of stem growth. These results highlight the functional trade-offs among genotypes and identify promising candidates for resilient carbon sequestration strategies under drought conditions.