The aim of the study was to evaluate the influence of various chemical forms of iodine (I− and IO3−) and selenium (SeO32− and SeO42−) on the nutritional and health-promoting quality of carrot (Daucus carota L.) storage roots. The experiment (conducted in 2012-2014) comprised the soil fertilization of carrot ‘Kazan’ F1 in the following combinations: 1. Control, 2. KI, 3. KIO3, 4. Na2SeO4, 5. Na2SeO3, 6. KI + Na2SeO4, 7. KIO3 + Na2SeO4, 8. KI + Na2SeO3, 9. KIO3+ Na2SeO3. Iodine and selenium were applied twice: before sowing and as top dressing in a total dose of 5 kg I ha−1 and 1 kg Se ha−1. No significant influence of iodine and selenium fertilization was noted with respect to average root weight and leaf yield. Each year, the application of KI + Na2SeO4 negatively affected the content of glucose and total sugars in carrot. An increased sucrose level was noted in the roots of plants treated with KIO3 + Na2SeO4, with a total sugar concentration comparable to the control. Irrespective of the year, carrots fertilized with KI were characterized by the highest accumulation of nitrates (III) – NO2− in roots. The simultaneous introduction of iodine and selenium compounds (KI + Na2SeO4, KIO3 + Na2SeO4, KI + Na2SeO3 and KIO3 + Na2SeO3) into the soil reduced the content of nitrates (III) in carrot as compared to combinations with the individual application of these compounds. The influence of the tested factors on other analysed parameters (the content of dry weight, nitrates (V), chlorides, oxalates, citrates, free amino acids, carotenoids, phenolic compounds, phenylpropanoids, flavonols and anthocyanins as well as free radical scavenging activity (DPPH) was rather year-dependent.