The aim of this paper is to propose a methodology for supporting decision-making in the design stages of new buildings or in the retrofitting of existing heritages. The focus is on the evaluation of economic–environmental sustainability, considering the presence of risk and uncertainty. An application of risk analysis in conjunction with Life-Cycle Cost Analysis (LCCA) is proposed for selecting the preferable solution between technological options, which represents a recent and poorly explored context of analysis. It is assumed that there is a presence of uncertainty in cost estimating, in terms of the Life-Cycle Cost Estimates (LCCEs) and uncertainty in the technical performance of the life-cycle cost analysis. According to the probability analysis, which was solved through stochastic simulation and the Monte Carlo Method (MCM), risk and uncertainty are modeled as stochastic variables or as “stochastic relevant cost drivers”. Coherently, the economic–financial and energy–environmental sustainability is analyzed through the calculation of a conjoint “economic–environmental indicator”, in terms of the stochastic global cost. A case study of the multifunctional building glass façade project in Northern Italy is proposed. The application demonstrates that introducing flexibility into the input data and the duration of the service lives of components and the economic and environmental behavior of alternative scenarios can lead to opposite results compared to a deterministic analysis. The results give full evidence of the environmental variables’ capacity to significantly perturb the model output.