Although cassava (Manihot esculenta Crantz) is regarded as an important food and energy crop, the effects of its cultivation on greenhouse gas (GHG) emissions remain poorly documented. This study, conducted in a tropical red Oxisol in Cambodia, quantified the effects of long-term cassava-based cropping systems on soil methane (CH4) and nitrous oxide (N2O) emissions using static chambers over two years (2022–24). Also accounting for measured change in soil organic carbon (SOC) stocks, the greenhouse gas balance (in CO2-eq) of the systems was determined. Established in 2009, the replicated treatments included: (1) conventional tillage mono-cropping cassava (CTM-Cs), (2) no-till mono-cropping cassava with biomass retention (NTM-Cs), and (3) no-till bi-annual cassava-maize rotation with cover crops (NTR), where cassava (Cs) and maize (Mz) are grown in two separate plots: NTR1 and NTR2. CH4-C emissions ranged from –123 to +141 µg CH4-C m–2 hr–1, with negligible cumulative emissions (–1.76 to +0.94 kg CH4-C ha–1 yr–1), depending on cropping systems and season. In cassava treatments, N2O-N emissions peaked after mineral fertilizer application (up to +141 µg N2O-N m–2 hr–1), while maize treatment showed the higher peaks (up to +437.18 µg N2O-N m–2 hr–1) after cover crop termination under NTR. Cassava treatments had lower (p 0.05) than CTM-Cs and NTM-Cs, respectively. Accounting for CH4 and N2O emissions and annual SOC accumulation, NTM-Cs, NTR1 and NTR2 systems (2022–24) resulted in a net climate mitigation benefit by sequestering –3.52, –1.93 and –3.16 Mg CO2-eq ha–1 yr–1, respectively. Our results showed that while N2O emissions were consistently higher in the treatment characterized by greater cover crop residue quantity and quality, they only slightly offset the climate benefits due to increased SOC stocks. Overall, the findings underscore the potential of NT systems for sustainable cassava production and climate change mitigation.