The aim of the study was to assess the nutritional value of H. tuberosus tubers grown in the organic farming system in Poland and Lithuania. The work was based on field experiments carried out in 2015–2017 in Parczew (Poland) and Akademija (Lithuania). The experiments were carried out using the randomized block method in four replications. Two cultivars of Jerusalem artichoke (JA) ‘Albik’ and ‘Rubik’ were tested. After the harvest of tubers, an assessment of their quality was carried out by standard methods. Due to the relocation of JA cultivation from Central and Eastern Europe to Northeast Europe, there were changes in the chemical composition of H. tuberosus tubers. The tubers from crops in Lithuania were characterized by a lower content of inulin, crude fiber and protein, ascorbic acid, total and endogenous amino acids than in Poland, but a higher content of true protein and macroelements. Edaphic factors determined, to a greater extent than genetic factors, the nutritional value of tubers. Assessment of the influence of varietal characteristics, meteorological conditions, and geographic location on the amount of biologically active compounds in JA will allow growers and consumers to choose the most suitable cultivars.