Quantifying greenhouse gas (GHG) emissions and setting GHG emissions budgets for anthropogenic systems are influenced by several value and modeling choices. This study, for the first time, quantified the influence of choice of GHG accounting approach, GHG metric, time horizon, climate threshold, global emissions budget calculation method, and effort-sharing approach, taking New Zealand (NZ) as a case study. First, NZ's production- and consumption-based emissions were quantified using multiregional input-output analysis and applying different GHG metrics (global warming and temperature potentials) and time horizons (20 and 100 years). Second, global emissions budgets for 1.5 °C, 2 °C, and 1 W m-2 climate thresholds were estimated. Budget shares were then assigned to NZ using two effort-sharing approaches (grandfathering and economic value), and emissions were benchmarked against the assigned shares. Finally, the analysis was undertaken at the NZ sector level. The results showed that, for each GHG accounting approach, NZ's total emissions exceeded their budget shares, irrespective of the choices; the largest source of uncertainty was the choice of global emissions budget calculation method, followed by GHG metric, climate threshold, effort-sharing approach, and reference year for the grandfathering approach. The sector-level analysis showed that, while most sectors exceeded their budget shares, some performed within them. The ranking of uncertainty sources was quite different at the sector level, with the choice of effort-sharing approach providing the largest source of uncertainty. Overall, the study indicates the importance of handling value and modeling choices in a transparent way when quantifying GHG emissions and setting emissions budgets for anthropogenic systems.