Pontechium maculatum (Russian bugloss) is a medical plant belonging to the family Boraginaceae. Although this species is known as a medical plant rich in biologically active secondary metabolites, biotechnological studies about this valuable plant is still missing. The scientific objectives of this study were to investigate the biomass production, synthesis, and productivity of various phenolic acids, flavonoids, and shikonin in P. maculatum cultivated in various breeding systems. Additionally, the antioxidant activity of plant-derived extracts was evaluated. Plants were cultivated in a traditional agar-solidified medium, a liquid medium with rotary shaking, and a temporary immersion bioreactors Plantform™ (TIB), as well as cultivated in soil (ex vitro conditions). Analyses of the growth index and dry weight accumulation were performed on the collected material. In the extracts obtained from examined plants, total phenolic content was estimated, and qualitative and quantitative analysis of phenolic derivatives using DAD-HPLC was conducted, simultaneously with an analysis of antioxidant capacity. TIB stimulated the highest synthesis of all examined phenolic acids and shikonin. In TIB-cultivated shoots level of rosmarinic acid obtained a concentration of 3160.76 mg × 100 g− 1 dry weight (DW), and shikonin obtained a concentration of 77.26 mg × 100 g− 1 DW. Furthermore, plants from TIB were characterized by the highest productivity of all studied phenolic derivatives, what makes it very effective platform for the synthesis of biologically active secondary metabolites in Russian bugloss. Moreover, this article shows that P. maculatum is a rich source of various phenolic derivatives with high antioxidant potential.