Salinity stress (SS) is major abiotic stress that is seriously limiting crop production across the globe. The application of organic amendments (OA) mitigate the effects of salinity and improves soil health and crop production on a sustainable basis. However, limited studies are conducted to determine the impact of farmyard manure (FYM) and press mud (PM) on the performance of rice crop. Therefore, we performed this study to determine the impacts of FYM and PM on the growth, physiological and biochemical attributes, yield, and grain bio-fortification of rice crop under SS. The experiment was comprised of SS levels; control, 6 and 12 dS m−1 SS and OA; control, FYM: 5%, press mud 5% and combination of FYM (5%) + PM (5%). Soil salinity imposed deleterious impacts on the growth, yield, and grain quality of rice, however, OA appreciably offset the deleterious impacts of SS and improved the growth, yield, and grain bio-fortification of rice crop. The combined application of FYM + PM improved the growth and yield of rice through an increase in chlorophyll contents, leaf water contents, anti-oxidant activities (ascorbate peroxidise: APX; catalase: CAT, peroxidise: POD and ascorbic acid: AsA), K+ accumulation and decrease in Na+/K+ ratio, electrolyte leakage, malondialdehyde (MDA), hydrogen peroxide (H2O2), Na+ accumulation. Moreover, the combined application of FYM + PM significantly improved the grain protein (5.84% and 12.90%), grain iron (40.95% and 42.37%), and grain zinc contents (36.81% and 50.93%) at 6 and 12 dS m−1 SS. Therefore, this study suggested that the application of FYM and PM augmented the growth, yield, physiology, biochemistry, and grain bio-fortification of rice and proved to be a good practice for better rice production in salt-affected soils.