Crops grown in seleniferous soil may accumulate selenium (Se) to levels considered highly toxic for animal and human consumption. Furthermore, higher Se content in plant tissues leads to considerable deterioration in product quality. Application of organic amendments plays an important role in improving soil physical, chemical, and biological conditions and influencing nutrient availability. A field trial was conducted to evaluate the effect of organic amendments, namely poultry manure (PM), sugar cane press mud (SCPM), and farmyard manure (FYM), on Se uptake and grain quality of wheat and oilseed rape grown on a seleniferous soil in Punjab, India. Selenium accumulation by wheat and oilseed rape grains decreased significantly (75%–95%) with the application of PM and SCPM, while FYM application resulted in a significant decrease (23%) only in case of wheat grains. The amount of Se associated with seed proteins varied in proportion to its uptake under different treatments. Quality of wheat grains improved considerably with respect to total soluble sugars, reducing sugars, starch, lipids, and sulfur concentrations only after application of SCPM and PM. Treating a Se‐contaminated soil with organic amendments significantly increased the oil concentration and changed the proportion of various fatty acids in rape grains. It is concluded that applying organic amendments to Se‐contaminated soils can alleviate the deleterious effects of Se and restore the nutritional quality of grains.