This study aim to evaluate the distribution of bioactive compounds in the tubers of organically grown Jerusalem artichoke (JA) during the growing season in 2012–2014. Field experiments on the three JA cultivars: Albik, Rubik and Sauliai, were carried out at the organic farm in South Lithuania. The tubers were uprooted at the end of each month of the growing period (8 times) in March–June (spring period) and August– November (autumn period) and were analysed for the contents of dry matter, carbohydrates, phenolic compounds, leuco-anthocyanins, catechins. The significantly highest dry matter content in JA tubers was determined in March of 2014 after they had been exposed to sub-zero temperatures in the soil during the winter, while the amount of phenolic compounds – at the beginning of the spring growing period. The significantly highest content of inulin in October of 2014 was accumulated in the tubers of cv. Sauliai (46.08%), carbohydrates – in Albik tubers in September of 2014 (44.23%), when the formation of new tubers began. Significantly higher amounts of catechins were determined in the second half of the growing period. Cultivar and organogenesis stage had a significant impact on the content of leuco-anthocyanins in JA tubers. Substantial differences in the content of leuco-anthocyanins among the tested cultivars were determined at the end of the growing season.