Land-use decision making in densely populated cities is challenged to cover the urban demand for water and food while maintaining the integrity of ecosystems that regulate the supply of these ecosystem services, beyond urban limits. Land-use decision making can be informed using spatial analysis of ecosystem services supply and demand, shedding light on potential mismatches, surpluses, deficits, and unsustainable uses of ecosystems. The integration of such analysis in land-use decision making, however, can be challenged by the complexity of the hierarchical and inflexible planning models used in various countries. We explored how the analysis of potential mismatches, surpluses, and deficits in the supply and demand of water and fertile soil can be spatially assessed for urban areas, and how such information can be used to inform land-use decision making. We used official data and geoprocessing methods to map water -supply, demand, and risk for water scarcity-, and fertile supply –supply, demand, and risk for food insecurity-, for Bogota and Villavicencio. We showed a high risk for water scarcity in Bogota, and an increasing competition for fertile soil between urbanization and agriculture. We recommended a cooperative management strategy of ecosystems and services considering that both cities shared river basins and natural reserves, in addition to their strike differences in population size. Inter-jurisdictional and inter-municipal cooperation, in addition to strong governance, are necessary to handle mismatches of urban ecosystem services supply and demand, and a potential solution to solve conflicts related to access, availability, and jurisdiction of ecosystem services in urban areas..