This research proposes a new distribution system of goods in the historical center of the city of Santiago, Chile. For the design of the urban logistic system, the methodology city logistics and last mile are used. This design incorporates to the freight transport flexible solutions that improve the efficiency of the distribution process and trade supply, minimizing the environmental impact of the atmospheric pollution (AP). The proposal was made through the data collection, the characterization of the sector and the diagnosis of the urban logistics processes. The analysis of the factors allowed to evaluate the costs of the AP negative externalities. The causes were used as design criteria for the proposals, with the aim of improving the quality of life of the city users. The physical location selection of the Cross-Docking was made through an optimization model of maximum coverage. The optimization algorithm of the nearest neighbor was proposed for vehicle routing. The analytic hierarchy process (AHP) was used to generate a ranking of the best non-polluting vehicles to be used in the zone. Finally, the results obtained allowed a 53 ton decrease in carbon dioxide in the square kilometer and reduced 1103 h of interruptions per year in the vehicular congestion of the sector.