Methods for threshing crops by magnetically treating the freshly threshed seeds in order to alter their biophysical, biochemical and physicochemical properties. The methods can be used in agriculture to magnetize seeds when threshing different types of crops during harvesting. In the crop threshing method which includes threshing to separate the mass of grain and chaff into an edible portion and a non-grain portion of the crop, the freshly threshed edible portion of the harvest is magnetically treated during the threshing process using a classic beater-type threshing drum. Magnetic treatment of the edible portion of the crop increases the germinating ability, yield and quality of crops and extends their storage life without loss of quality.