The use of saline water for the irrigation of forage crops to alleviate water scarcity has become necessary in semi-arid and arid regions and researchers have been seeking ways to offset the harmful results of soil salinity. Soil amendments with compost, manure and other organic material provide a valuable source of plant nutrients and appear to speed up soil recovery. The aim of this study was to compare the benefits of farmyard manure and a municipal solid waste (MSW) compost (40 mg ha−1) for raising alfalfa (Medicago sativa, cv. Gabès) under salt-water irrigation. Both compost and manure improved plant mineral uptake and growth of alfalfa cultivated in clay soil. Using compost in clay soil increased the content of copper (Cu), cadmium (Cd), and zinc (Zn) in plant tissues compared to manure, while the bio-accumulation factor (BAF) of Cu, Pb and Zn was higher in plants grown with manure compared to MSW compost with salt stress. Compost addition could enhance alfalfa growth under salt stress, which depends on salt doses and can greatly improve the recovery effects in a cost-effective way, although additional amendment type should receive special attention in order to be used as a tool for sustainable agriculture.