Many people around the world struggle with the problem of an insufficient supply of iodine (I) and selenium (SE) in their diet. Food enriched with these elements is a good source of iodine and selenium. Juices made from four carrot (CJ) cultivars and biofortified with iodine and selenium (BCJs) were investigated to determine their I and Se contents, their impact on the supply of these elements to the diet, and losses in the production process. Other juice parameters important for consumers health were also determined. A significant increase in I and Se content relative to CJ was observed for each BCJ. The losses of I and Se (relative to raw material) during juice preparation were depended based on variety and added elements. Carrot biofertilization with iodine and selenium contributed to decreased contents of dry matter, total soluble solids, protein, sugars, and β-carotene in the juices and lower antioxidative activity as compared with CJ. Biofortification had little effect on the color and pH of juices. Finally, six polyphenolic compounds were identified and determined. Despite the reduction in the content of some ingredients in BCJ, they still remain their valuable source. Their added value is the increased content of iodine and selenium, which largely cover the daily demand for these elementals.