In the last decade, many studies focused on finding optimal design solutions considering trade-offs between different aspects of building design. Accordingly, multi-objective optimization (MOO) approaches have been increasingly applied in the building industry. However, certain aspects must be deepened to ensure a more effective decision-making process in the early planning phase. On the one hand, uncertainties should be considered before making decisions to ensure the robustness of the optimal solutions; on the other hand, decisions are made at different times in building planning, and the sequential order of making decisions should be modeled. This paper presents a holistic two-stage multi-objective stochastic optimization (MOSO)-II framework to minimize the environmental impact of global warming potential (GWP) and cost throughout the entire life cycle of a building (phases of A1-A3, B4, B6 and C3-C4), considering passive and active design strategies in two consecutive stages, under uncertainty. Herein, individual/use and political/market uncertainties are considered. As a proof of concept, the proposed framework is applied in a case study for a generic zone in a multi-family terraced residential building type with solid brick construction. The advantages of the proposed framework are validated by comparing it with alternative single-stage MOSO frameworks. Results show that the proposed two-stage MOSO-II framework can deliver a smaller range of solutions with a better performance in terms of lower GWP and cost. It indicates that the proposed framework can effectively assist planners in decision-making by reducing the effort in choosing the proper solution. Secondly, the results also emphasize the importance of passive design strategies in sustainable building planning. In addition, the energy mix structure and cost of energy sources should be carefully adjusted in the future to promote a more ecologically sustainable building design.