A methodical approach for the determination of economic and socio-environmental costs in the application of the city consolidation center at the micro level was proposed and tested on real data. Two options of urban delivery of small shipments are considered, in particular, for e-commerce - direct delivery and delivery through the micro-consolidation center. The system of indicators proposed in this work allows a detailed assessment of the economic component of direct and consolidated delivery, including transportation costs, the functioning of the consolidation center costs and costs for pedestrian delivery to the residential district customers. Socio-economic indicators allow considering the interests of other residents of the city, suffering from a dense traffic flow and harmful emissions from freight vehicles. The proposed method of integrated assessment was tested on real data of a micro district of the city. The results made it possible to estimate the proportion of each component of expenditures in the economic, socio-environmental and total costs for both delivery options. The analysis of the sensitivity of costs to changes in the input parameters showed the difference in the strength of influence, and the rating of influencing factors. The proposed method allows us to estimate the economic costs of all participants in the urban delivery process for small shipments, as well as to prove the rationality of using micro-consolidation to serve a micro district of a large city.