This paper describes the methodology used to spatially and temporally disaggregate carbon dioxide emission estimates for the City of Cape Town, to be used for a city-scale atmospheric inversion estimating carbon dioxide fluxes. Fossil fuel emissions were broken down into emissions from road transport, domestic emissions, industrial emissions, and airport and harbour emissions. Using spatially explicit information on vehicle counts, and an hourly scaling factor, vehicle emissions estimates were obtained for the city. Domestic emissions from fossil fuel burning were estimated from household fuel usage information and spatially disaggregated population data from the 2011 national census. Fuel usage data were used to derive industrial emissions from listed activities, which included emissions from power generation, and these were distributed spatially according to the source point locations. The emissions from the Cape Town harbour and the international airport were determined from vessel and aircraft count data, respectively. For each emission type, error estimates were determined through error propagation techniques. The total fossil fuel emission field for the city was obtained by summing the spatial layers for each emission type, accumulated for the period of interest. These results will be used in a city-scale inversion study, and this method implemented in the future for a national atmospheric inversion study.