This study presents a conceptual framework proposal for integrating urban freight initiatives (UFIs), or city logistics initiatives, into urban planning and urban management (UPUM) land use and infrastructure systems. As a novel approach, this framework integrates three components: Firstly, a conceptual basis on three economic geography theory principles—location, agglomeration, and urbanisation. Secondly, spatial analysis and subsequent clustering integrate companies’ spatial positions, their proximity to other companies, their freight intensity, and the characteristics of the zonal road infrastructure; these clusters are defined as freight traffic zones (FTZs). Thirdly, a functional yet strategic UFI clustering or grouping is proposed to work in an optimised and integrated manner with the FTZs’ opportunities for efficiency and reduced externalities. It is expected that the integrated result of these three components can serve to optimise freight initiatives and road infrastructure from a city governance perspective, reduce freight externalities, and function as a stakeholder cooperation tool from government-led, policy-driven perspectives. This research also identifies and characterises various variables influencing the emergence and existence (planned or organic) of FTZs and shows how these could be incorporated into high-level UPUM processes. Although it is deemed that the principles and methodological approach followed here could be common to urban areas, an example for the Metropolitan Area of the Aburra Valley (MAAV), in Colombia, is presented as an initial case study. Conclusively, this paper introduces a pioneering methodology for integrating UFIs into city or metropolitan governance, offering guidance for policymakers to promote sustainable freight systems.