The implementation of changeable and reconfigurable manufacturing systems and realization of benefits connected to rapid, efficient, and dynamic change of functionality and capacity is key to achieve manufacturing competitiveness. Therefore, this paper proposes a systematic methodology for the design and development of changeable and reconfigurable manufacturing systems, derived from design theory, reconfigurability theory, as well as practical experience. The methodology consists of a concrete course of actions that connects design phases and working steps based on the content of the design task. Furthermore, the paper addresses project-related and contextual aspects of reconfigurability development, which indicates how the proposed methodology should be adapted to the specific company and task at hand. Thus, the proposed methodology is intended for further validation in different types of manufacturing companies that are transitioning towards reconfigurability.