The Energy Performance of Buildings Directive (EPBD) mandates European Union Member States (MS) to conduct cost-optimal studies using the national calculation methodology (NCM), typically through non-calibrated asset-rating software. Nearly zero-energy building (NZEB) levels must be derived for each chosen Reference Building (RB), which are generally defined using deterministic parameters. Previous research proposed an innovative cost-optimal method that replaces ‘non-calibrated deterministic RBs’ with ‘probabilistically Bayesian calibrated reference building (RB)’ to better handle building stock uncertainties and diversities when deriving benchmarks. This paper aims to develop a framework to address two research gaps necessary for the successful application of the innovative cost optimal method: (1) providing objective criteria for defining NZEB benchmarks and (2) propagating uncertainties and financial risk for each defined benchmark. A robust approach for defining NZEB benchmarks according to four different ambition levels (low, medium, high, and highest) was developed by objectively considering distinct points from multiple cost-optimal plots employing different financial perspectives. Risk analysis is then performed for each defined benchmark by propagating risk from the posterior calibration parameter distributions to visualize and statistically quantify the financial risk, including robust risk, that the private investor could face for reaching each derived benchmark ambition level. The innovative cost-optimal methodology that incorporates the developed framework was applied to a hotel RB case study. The results showed that the developed framework is capable of deriving distinct benchmarks and quantitatively uncovering the full financial risk levels for the four different renovation ambition levels. The current cost-optimal method was also performed for the hotel case study with the RB defined determinitically and using the non-calibrated NCM software, SBEM-mt v4.2c. It was found that the financial feasibility and energy-saving results per benchmark are significantly more realistic and transparent for the proposed innovative cost-optimal method including a better match between the simulated and metered energy consumption with a difference of less than 1% in annual performance. Thus, the performance gap between calculated and actual energy performance that is synonymous with the EPBD methodology, as reported in the literature, is bridged. The case study also showed the importance of the risk analysis. Performing the cost-optimal analysis for a Bayesian calibrated RB using the mean value of the posterior calibrated parameter distributions without propagating uncertainty produced highly optimistic results that obscured the real financial risk for achieving the higher ambition levels of the NZEB benchmarks. Consequently, the developed framework demonstrated a time-bound tightening approach to achieve higher energy performance ambitions, improve risk transparency to private investors, and facilitate more targeted policies towards a net zero-carbon status. Thus, the proposed method considering parameter uncertainty and calibrated RBs is instrumental for devising robust policy measures for the EPBD, to achieve a realistic and long-lasting sustainable energy goal for European buildings.