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Aligning construction activities with climate goals requires the use of carbon budgets. However, uncertainties and allocation choices surrounding these budgets, such as fairness principles and development assumptions (e.g., rate of new constructions and renovations or share of imports), pose challenges. The research questions of this study address the extent of uncertainties’ influence on building-level targets and how to effectively consider them at a policy level. The study employs a sensitivity analysis on input parameters defining top-down building budgets. Results show that fairness principles significantly impact budget allocations and target definitions; nevertheless, the choice remains at political and societal level. In Switzerland, embodied targets are highly sensitive to the share of emissions from imported materials making it a controversial parameter in the model. The volume and impact variability of new construction and renovation activities moderately affect the building-level targets and are interdependent (the more budget for new constructions, the lower for renovations). The constructive consequences of the uncertainties behind carbon budgets allocation mean that design options can either be restricted to unfeasible constraints or be viable to laxed construction practices. Carbon budgets for buildings are crucial for aligning construction activities with net-zero pathways, but they must be responsive to market changes and policy developments. Stakeholders should employ a combination of top-down and bottom-up approaches to comprehensively evaluate targets’ viability and inform decision-making. Understanding and managing the inherent variability of uncertainties are vital for effective decision-making throughout the design process.