Intensification of homegardens in the Nuba Mountains may lead to increases in C and nutrient losses from these small-scale land-use systems and potentially threaten their sustainability. This study, therefore, aimed at determining gaseous C and N fluxes from homegarden soils of different soil moisture, temperature, and C and N status. Emissions of CO2, NH3, and N2O from soils of two traditional and two intensified homegardens and an uncultivated control were recorded bi-weekly during the rainy season in 2010. Flux rates were determined with a portable dynamic closed chamber system consisting of a photo-acoustic multi-gas field monitor connected to a PTFE coated chamber. Topsoil moisture and temperature were recorded simultaneously to the gas measurements. Across all homegardens emissions averaged 4,527 kg CO2-C ha−1, 22 kg NH3-N ha−1, and 11 kg N2O-N ha−1 for the observation period from June to December. Flux rates were largely positively correlated with soil moisture and predominantly negatively with soil temperature. Significant positive, but weak (rs < 0.34) correlations between increasing management intensity and emissions were noted for CO2-C. Similarly, morning emissions of NH3 and increasing management intensity were weakly correlated (rs = 0.17). The relatively high gaseous C and N losses in the studied homegardens call for effective management practices to secure the soil organic C status of these traditional land-use systems.