Nitrogen (N)-fixing tree and crop intercropping systems can be a sustainable agricultural practice in sub-Saharan Africa and can also contribute to resolving climate change through enhancing soil carbon (C) sequestration. A study conducted by Makumba et al. (Agric Ecosyst Environ 118:237–243, 2007) on the N-fixing tree gliricidia and maize intercropping system in southern Malawi provides a rare dataset of both sequestered soil C and C loss as soil carbon dioxide (CO2) emissions. However, no soil C gain and loss estimates were made so the study failed to show the net gain of soil C. Also absent from this study was potential benefit or negative impact related to the other greenhouse gas, nitrous oxide (N2O) and methane (CH4) emissions from the intercropping system. Using the data provided in Makumba et al. (Agric Ecosyst Environ 118:237–243, 2007) a C loss as soil CO2 emissions (51.2 ± 0.4 Mg C ha−1) was estimated, amounting to 67.4% of the sequestered soil C (76 ± 8.6 Mg C ha−1 in 0–2 m soil depth) for the first 7 years in the intercropping system. An annual net gain of soil C of 3.5 Mg C ha−1 year−1 was estimated from soil C sequestered and lost. Inclusion of the potential for N2O mitigation [0.12–1.97 kg N2O–N ha−1 year−1, 0.036–0.59 Mg CO2 equivalents (eq.) ha−1 year−1] within this intercropping system mitigation as CO2 eq. basis was estimated to be 3.5–4.1 Mg CO2 eq. ha−1 year−1. These results suggest that reducing N2O emission can significantly increase the overall mitigation benefit from the intercropping system. However, significant uncertainties are associated with estimating the effect of intercropping on soil N2O and CH4 emissions. These results stress the importance of including consideration of quantifying soil CO2, N2O and CH4 emissions when quantifying the C sequestration potential in intercropping system.