Abstract In the past 10 years, 90% of cassava starch factories in Thailand have switched from fuel oil to renewable biogas, to cover part of their energy needs. The environmental benefits of switching to biogas have not been assessed quantitatively. To alleviate this, this study assessed 100-year greenhouse gas (GHG) emissions, or carbon footprint (CF), of cassava starch production for four factories in Thailand. Key results demonstrate that biogas reduces the carbon footprint of the Thai cassava starch industry as a whole by 0.9–1.0 million tons CO2eq/year, and highlight methodological precautions to collect LCI data and allocate GHG emissions between co-products with high moisture contents. The system boundaries included farm stage (production of cassava roots), transportation to factory and processing into native starch. The functional unit (FU) was one ton of native cassava starch at 13% water content. Biogas produced from the factory wastewater (95–200 m3/FU) was the main source of thermal energy for starch drying, and for on-site electricity production when excess biogas was available. The total CF of cassava starch was in the range 609–966 kg CO2eq/FU. Agricultural production contributed 60% of the carbon footprint, mainly from the use of nitrogen fertilizers. GHG emissions of root production varied widely due to (1) the diversity of farming practices even within a small radius (50 km), and (2) different agricultural yields in different regions. The contribution of the factory stage to the carbon footprint depended on the use of electricity, biogas and other fuels, ranging from 217 to 342 kg CO2eq/FU. Allocation rules such as wet weight or dry weight basis allocations affected the results markedly.