Anthropogenic climate change has caused increased soil salinity in South Asia due to saltwater intrusion caused by sea level rise, input of fertilizers with high salt index, and irrigation malpractices, etc. Salinity has a multitude of impacts on plant and soil processes, leading to alterations in gas fluxes and rice productivity. The remedial measures adopted on salt-affected soils to reduce the salinity effect could enhance future climate change if they cause an increase in greenhouse gas (GHG) emissions. This study was conducted to find the best agricultural management practices (BMPs) for salt-affected soils in rice cropping systems (i.e. the major cropping system in Asia) in four South Asian countries (Sri Lanka, India, Bangladesh and Pakistan) considering net GHG emissions and other socioeconomic benefits associated with the adopted measures. The salinity-affected sites were selected based on available information (e.g. agricultural statistics and maps). Site-level measurements on soil parameters and GHG emissions were made in control- and managed plots and farmer surveys were conducted. Although organic amendments ameliorated salinity, it could cause a net increase in carbon dioxide or methane emissions depending on the soil conditions, particularly during the initial stages. This impact could be ameliorated by combining organic amendments with other management practices. In the Indo-Gangetic region, poor soil drainage causing anaerobic conditions favoured nitrous oxide emission under low to medium salinity. Yield losses and emissions in high salinity sites were controlled through organic amendment, irrigation and rice-fallow cropping sequence. The combination of transplanting of rice seedlings, the addition of organic matter, and intermittent irrigated water levels was identified as the BMP for Sri Lankan farmers. The outcome of this project will be used to raise awareness among farmers and policymakers.