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Salt affected soils either developed from parent material (primary) or from anthropogenic activities (secondary) extended in arid and semi-arid regions reduced the crop growth. An increasing trend of salt affected soils is a major risk for food security and sustainable agriculture. The adverse effect of salt stress on crop growth is related with the specific ion toxicity, low osmotic potential and nutritional imbalance. Salt stress damages the soil physical properties that can be improved by addition of organic amendments such as municipal solid waste compost (MSWC). MSWC is eco-friendly, adds organic matter in soil and compensate the mineral fertilizer. Field experiments were conducted to assess the site-specific nutrient management using MSWC in rice-wheat cropping system under salt affected conditions. Application of inorganic and organic content (MSWC) keeping in consideration the P-fixation capacity of soils and site-specific nutrient management approach can improve the crop yields. Results revealed that site-specific use of mineral fertilizer with MSWC and integrated use of chemical fertilizers with MSWC in 80:20 ratio improve the paddy/grain yield and soil health. Site-specific and integrated use of chemical fertilizer with MSWC in 80:20 ratio produced the highest biomass / paddy and biomass/grain yield i.e. 11.04/2.67 and 5.62/2.70 Mg ha(-1) at Kot Murad, District Hafizabad, respectively. Pre-sowing and postharvest soils analysis was carried out after transplanting/sowing of each crop. Integrated and site specific use of MSWC slightly reduced the salinity/sodicity than the initial status of soil while organic matter, available P, extractable K and Zn were increased compared to initial values.