Management intensification has raised concerns about the sustainability of homegardens in the Nuba Mountains, Sudan. This study aimed at assessing the sustainability of these agroecosystems following the approach of carbon (C) and nutrient balances. Three traditional (low input) and three intensified (high input) homegardens were selected for monitoring of relevant input and output fluxes of C, nitrogen (N), phosphorus (P) and potassium (K). The fluxes comprised those related to management activities (soil amendments, irrigation, and biomass removal) as well as estimates of biological N-2 fixation, C fixation by photosynthesis, wet and dry deposition, gaseous emission, and leaching. Annual balances for C and nutrients amounted to -21 kg C ha(-1), -70 kg N ha(-1), 9 kg P ha(-1) and -117 kg K ha(-1) in high input homegardens and to -1,722 kg C ha(-1), -167 kg N ha(-1), -9 kg P ha(-1) and -74 kg K ha(-1) in low input homegardens. Photosynthesis C was the main C input flux with averaged of 7,047 and 5,610 kg C ha(-1) a(-1) in high and low input systems, respectively. Biological N-2 fixation (17 kg N ha(-1) a(-1)) was relevant only in low input systems. In both systems, the annual input of 77 kg K ha(-1) through dust was highly significant and annual gaseous C losses of about 5,900 kg C ha(-1) were the main C loss. In both garden types, the removal of biomass accounted for more than half of total nutrient exports of which one-third resulted from weeding and removal of plant residues and two-third from harvest. The observed negative nutrient balances may lead to a long-term decline of crop yields. Among other measures the reuse of C and nutrients in biomass removals during the cleaning of homegardens may allow to partially close C and nutrient cycles.