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The COVID-19 pandemic outbreak deeply impressed supply chains in different aspects. In response to this unexpected situation, supply chain managers have decided to recover and reinforce their supply chains. Considering the expanse of these decisions, project management principle and tools seems inevitable to successfully manage the transformation from before pandemic to post-pandemic supply chains (SCs). In this study, the problem of time–cost tradeoff is extended to time, cost, and risk tradeoff. The risk factor is considered to convey the uncertainty arising from the COVID-19 pandemic situation. Since projects are affected by the level of pandemic expansion and different countries ruled out various quarantine policies (isolation, quarantine, social distancing, and lock-down), the tradeoff problem is influenced accordingly. Therefore, a scenario-based robust optimization model is proposed to deal with time, cost, and risk tradeoff problems to reflect the effects of the global pandemic of COVID-19 on managing projects in supply chains. In addition, various quarantine policies (isolation, quarantine, social distancing, and lock-down) as a prevalent response to the pandemic have been investigated separately. To illustrate the model, a real-world case study in the emerging economy of Iran is examined using the proposed approach. The results indicated that supply chain managers can use the designed model and approach as a tool for a flexible and adaptable decision-making framework dealing with a global pandemic such as COVID-19.