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This paper presents a methodology to design interoperable lean, agile, resilient, and green industrial ecosystems based on axiomatic design. The main objective is to develop a systematic approach to support the detailed design of collaborative business platforms that are able to deliver high level of interoperability, as measured by the expanded business interoperability quotient measurement model. To achieve this objective, axiomatic design is employed to develop the “ideal” cooperation configuration by defining and aligning a set of functional requirements necessary to establish an effective and efficient cooperation among networked organizations. The applicability of the developed methodology is tested through an application scenario of implementing reverse logistics among an automaker focal firm and its upstream partners, as well as some external stakeholders.