To mitigate the effects of catastrophic failure while maintaining resource and production efficiencies, energy systems need to be designed for resilience and sustainability. Conventional approaches such as redundancies through backup processes or inventory stockpiles demand high capital investment and resource allocation. In addition, responding to unexpected “black swan” events requires that systems have the agility to transform and adapt rapidly. To develop targeted solutions that protect the system efficiently, the supply chain network needs to be considered as an integrated multi-scale system incorporating every component from individual process units all the way to the whole network. This approach can be readily integrated with analogous multiscale approaches for sustainability, safety, and intensification. In this work, we bring together classical supply chain resilience with process systems engineering to leverage the multi-scale nature of energy systems for developing resilience enhancement strategies that are resource-efficient. In particular, we adapt qualitative risk analysis methods to uncover critical system components and major vulnerabilities to guide resource allocation decisions. To account for these vulnerabilities, we explore the feasible region of operation around each node of the supply chain. An optimization formulation is devised to generate multiscale alternative. The approach is demonstrated through a case study involving the production of biofuels, demonstrating the range of adaptation strategies possible when process-level strategies are incorporated into overall supply chain design.