Many industrial firms adopted a deterministic irreversible investment plans without any pro-active risk management strategy. The existing literature of the Supply Chain Design does not value the managerial flexibility as enabled by the Real Option (RO) theory. However, this latter considers only single project and not adapted to supply chain investments. This opens a new area of research. Thus, this paper is concerned with providing a practical and novel framework for de-risking future investments of large-scale, capital-intensive interdependent industrial projects, in an uncertain and risky environment. The suggested framework is based on real option analysis and aims to integrate managerial flexibility in terms of “real options” to efficiently adjust the investment plans to the evolution of uncertainties over time, considering interdependencies between projects, while reducing downside risks and increasing potential opportunities. This framework has been tested to assess potential risks, define and value flexible strategies to deal with the construction delays and the cost overruns in the investment planning of phosphates fertilizer firm. The insights indicate that flexibility lead to higher expected performance while reducing downside risks and raising potential upside gains.