This study introduces a systems-theoretic methodology to meet the requirements of a major national infrastructure for safety and security-based design by enhancing the alignment of stakeholders and actors in the project. Safe-by-Design (SbD) is an engineering concept for risk management that considers safety as much as possible in the design phase. The article presents the results of a case study conducted to investigate the efficacy of recent system safety models and analysis techniques in the major national infrastructure of a Waste-to-Energy (WtE) project under consideration in Iceland. The structures and roles within the system responsible for constructing the WtE plant, given the sustainability and circular economy restrictions, are addressed in the study. Stakeholders’ roles and responsibilities are analyzed, yielding their feedback on potential risks and creating a positive image of the project. Also, suitable ways to enter the project and finance it are devised. In essence, this enables the creation of a safety and security-based design approach. Furthermore, detailed documentation of the system model development is presented. The novelty of the study lies in the application of STAM, STPA, and STECA as an SbD approach for a major infrastructure project. Also, the methods discussed here have not been used in a WtE project as far as we know.