Scientific management of available resources in the most judicious manner ensures food security and protects the environment from further degradation. Integration of varied enterprises like field crops, horticultural / fruit crops, timber trees, green manures, fodder, livestock, poultry, fish and vermicompost in a farming system can improve the input use efficiency and carbon sequestration into soil and plant biomass. This helps in mitigating greenhouse gas emission (GHG) into the atmosphere. The present study was conducted with the objective to estimate net GHG emission from four integrated farming system (IFS) models developed in a research station attached to Kerala Agricultural University. Various farm activities carried out in each IFS model, the inputs supplied and output generated including the plant biomass (above and below ground) were considered for calculating the GHG emission and carbon sequestered in the farm. IPCC guidelines were followed in estimating GHG emission based on this Life cycle approach. In all the four IFS models, except rice based IFS model (799.1 kg CO2 equivalent), there was net negative GHG emission indicating the role of incorporated organic manures and crop residues and agroforestry component in fixing carbon into the system. Highest amount of carbon sequestration through agroforestry component resulted in homestead based IFS model while the lowest for rice based IFS (72836 and 1593 kg CO2 equivalent, respectively). The reverse trend was noticed for net GHG emission from the IFS models. Net GHG emission from homestead based IFS was -69421 kg CO2 equivalent.