Association of agriculture with climate change is widely established. Soil constituents and soil salinity along with the amendments for soil improvement are the key contributors in affecting this association. The present study targets the above issue to find the best management practice in terms of reduction in greenhouse gas (GHG) emissions in Indo-Gangetic plain of Uttar Pradesh. The six sites selected for the study varied in salinity level and followed different management practices of organic and inorganic amendments. Emissions of CO₂, CH₄ and N₂O from soil were measured at different stages of rice and wheat/ mustard/ fallow systems. The findings revealed that soil salinity, crop type and organic/ inorganic amendments differently affected the emission as the fluxes of GHGs varied at different stages of crop growth cycle at different sites. Salinity induced variations generally tended to reduce the CH₄ emission while increased the emission of CO₂ and N₂O, whereas organic matter amendment increased CO₂ and CH₄ fluxes in comparison to inorganic fertilizer application at the studied sites. The site with rice-mustard cropping exhibited the highest CO₂ and N₂O fluxes, measuring 3645 and 1.9 mg m^− 2 h^− 1, respectively. Conversely, the highest CH₄ flux of 0.873 mg m^− 2 h^− 1 was recorded at the saline rice-wheat cropping site. Electrical conductivity, moisture content, soil temperature and total organic carbon acted as major explanatory factors for soil emission of all the GHGs. Further exploration and experimentation are suggested with the use of different amendments to reduce GHG emissions in rice-wheat system, for greater sustainability potential. This ongoing research is vital for optimizing agricultural practices and enhancing their long-term environmental viability.