Salt-affected soil reclamation provides opportunities for crop production and carbon sequestration. In arid regions such as Pakistan, limited studies have been reported involving soil reclamation and crop production under wheat–maize rotation, but no study has reported predictions on long-term carbon sequestration in reclaimed soils for the treatments used in this study. Thus, a field-scale fallow period and crop production experiment was conducted for wheat–maize rotation on salt-affected soils in Pakistan for 3 years to check the effectiveness of organic amendments for reclamation of the salt-affected soils, carbon sequestration and food grain production. Treatments used were the control (with no additional amendments to reduce salinity), gypsum alone and gypsum in combination with different organic amendments (poultry manure, green manure, and farmyard manure). The treatment with gypsum in combination with farmyard manure was most effective at increasing soil carbon (+169% over the three-year period of the trial). The maximum wheat yield was also recorded in year 3 with gypsum in combination with farmyard manure (51%), while the effect of green manure combined with gypsum also showed a significant increase in maize yield in year 3 (49%). Long-term simulations suggested that the treatments would all have a significant impact on carbon sequestration, with soil C increasing at a steady rate from 0.53% in the control to 0.86% with gypsum alone, 1.25% with added poultry manure, 1.69% with green manure and 2.29% with farmyard manure. It is concluded that food crops can be produced from freshly reclaimed salt-affected soils, and this can have added long-term benefits of carbon sequestration and climate change mitigation.