The goal of this paper is to put the issue of preserving Soil Organic Matter (SOM) into a regional, urban-rural, context. In doing so, we apply the method of material flux analysis to a watershed in Boyacá in Colombia. We estimate the order of magnitude of the dry organic matter and carbon fluxes between the rural and urban parts of the region, including estimates on biomass growth, tillage, organic waste, and sewage. These estimates are used to derive potentials for carbon cycling between rural and urban areas. It is shown that (i) for the municipality of Tunja, the treated organic wastes produced in the urban area could add about 30% to the current carbon input into arable soils; (ii) to preserve the organic carbon content in soils in Tunja over the long-term, either, erosion control measures have to be implemented and/or the total treated urban organic wastes have to be concentrated on about 1/5 of the agricultural area. However, such an attempt has to consider the possible trade off between allocation needs (poor farmers on the hillside) and allocation costs (transportation and distribution costs).