Common centaury (Centaurium erythraea Rafn) is an important plant species in traditional medicine because it has been used for the treatment of numerous diseases since ancient times. Moreover, centaury is rich source of antioxidants and antimicrobial compounds and, as such, can be considered as a potential food additive. Considering that, in nature, centaury can often be found on moderately saline soils, it was interesting to investigate the effects of salinity stress, caused by sodium chloride (NaCl), on total phenolic, flavonoid, and hydroxycinnamic acid content and antioxidative capacity, in shoots and roots grown in vitro. Centaury shoots were cultured on a solid ½MS medium supplemented with graded NaCl concentrations (0, 50, 100, 150, and 200 mM). Centaury roots were also grown in vitro but in liquid ½MS medium containing the same graded NaCl concentrations. After eight weeks, the content of total phenolic, flavonoid, and hydroxycinnamic acid content and antioxidative capacity were determined using colorimetric methods. The results obtained in this work showed that graded NaCl concentrations induced the accumulation of total phenols in both shoots and roots. Regarding total flavonoid content, the graded NaCl concentrations also induced the accumulation of total flavonoids in roots, while in shoots the highest content was detected in the presence of 50 mM NaCl. On the other hand, the increment of NaCl in nutrient media promoted the accumulation of total hydroxycinnamic acid content in both shoots and roots, with the exception of roots grown in the presence of 200 mM NaCl. Finally, the DPPH test has shown an increased antioxidative capacity in shoots and roots, which was dependent on applied NaCl concentration. It can be concluded that salinity stress affected shoots and roots’ total phenolic, flavonoid, and hydroxycinnamic acid content differently but also elevated antioxidative capacity.