Circular economy and urban metabolism concepts have recently received great attention both in the political and academic arenas, starting a roll-over process of the “take, make, and dispose” dominant economic model that is leading to an ongoing increase of resource consumption and waste generation. However, there is a relative lack of guidelines for introducing such concepts in a decision-making process able to support the design of appropriate policies and strategies and the definition of specific actions to cope with such challenges. This paper attempts to contribute to the recent efforts at incorporating these concepts in policy and decision-making processes by providing a methodology for the development of strategic plans for waste prevention and resource management. The proposed methodology, developed within the Urban_WINS project, combines different quantitative–analytical and qualitative methods and tools, together with a participatory process. The methodology was tested in eight EU cities and allowed to formulate several measures and actions aimed at addressing the challenges posed by the current consumption patterns. Moreover, the participatory approach led to the legitimization of the strategic plans, as well as to raise awareness among stakeholders. Although it might require specific tailor-made adjustments, this methodology is suitable to be replicated in other contexts.