The present invention refers to compositions of atomized or lyophilized extracts of selected maca hypocotyls of the red and black variety and atomized or lyophilized parts of the yacon plant selected from leaves and roots. The invention also refers to the methods to prepare such compositions using aqueous or hydroalcoholic extraction processes. Likewise, as novel element of the maca hypocotyls extraction process is the selection of the batches of maca hypocotyls having a pH of less than 5.5, which have better biological activity than those with a greater pH. The compositions of the invention are useful in the treatment of different conditions and diseases.