The urgent need for sustainable development is imposing radical changes in the way manufacturing systems are designed and implemented. The overall sustainability in industrial activities of manufacturing companies must be achieved at the same time that they face unprecedented levels of global competition. Therefore, there is a well-known need for tools and methods that can support the design and implementation of these systems in an effective way. This paper proposes an engineering method that helps researchers to design sustainable intelligent manufacturing systems. The approach is focused on the identification of the manufacturing components and the design and integration of sustainability-oriented mechanisms in the system specification, providing specific development guidelines and tools with built-in support for sustainable features. Besides, a set of case studies is presented in order to assess the proposed method.