The growing interest of consumers in healthy organic products has increased the attention to the organic production of beetroot. In this regard, six field experiments were conducted in 2017 and 2018 in three different locations under the specific conditions of organic agriculture, and fifteen beetroot genotypes, including one F1 hybrid as a commercial control and one breeding line, were compared regarding the content of the total dry matter, total soluble sugar, nitrate, betalain, and total phenolic compounds in order to investigate the genetic potential of new and existing open-pollinated genotypes of beetroot regarding the content of their bioactive compounds. The results of this study indicated a significant impact of genotype (p < 0.05) on all measured compounds. Furthermore, results revealed a significant influence of the interactions of location × year (p < 0.05) on the beetroot composition, and, thus, the role of environmental conditions for the formation of tested compounds. The total dry matter content (TDMC) of beetroots varied between 14.12% and 17.50%. The genotype ‘Nochowski’, which possessed the highest total soluble sugar content with 14.67 °Bx (Brix), was among the genotypes with the lowest nitrate content. On the contrary, the cylindrical-shaped genotype ‘Carillon RZ’ (Rijk Zwaan), indicated the lowest sugar content and the highest nitrate concentration. The amount of total phenolic compounds ranged between 352.46 ± 28.24 mg GAE 100 g−1 DW (milligrams of gallic acid equivalents per 100 g of dry weight) and 489.06 ± 28.24 mg GAE 100 g−1 DW for the red-colored genotypes which is correlated with the high antioxidant capacity of the investigated genotypes. Due to the specifics of the required content of bioactive compounds for various products, the selection of suitable genotypes should be aligned with the intended final utilization.