The development of Latin American cities has been characterised by disorderly expansion. This urbanisation looks set to continue, and, by 2050, there will be a considerable demand for resources, spaces, and food to survive in emerging societies. All this requires an increase in urban freight logistics operations. Although several stakeholders are involved, citizens tend to be overlooked when planners and decision makers look to solve the problems generated by freight operations. This research focuses on logistics activities and stakeholder perceptions in areas of high vehicular flow and commercial establishment density in the mid-sized Colombian city of Popayán. Drawing on the methods proposed in previous studies conducted in Latin American cities, this paper’s scientific value lies in its comprehensive approach, integration of quantitative and qualitative data, and application of PLS-SEM analysis. Its contribution to sustainable urban planning is evident through insights into optimising urban logistics, enhancing stakeholder engagement, promoting sustainable transport, and informing policy formulation. These aspects make the paper a valuable resource for researchers, policymakers, and urban planners seeking to create more sustainable and efficient urban logistics systems. The results show a correlation between commercial establishments’ locations and urban logistics operations. Overall, the research creates an ample scope for studying stakeholder perceptions and urban logistics in other mid-sized Latin American cities.