The main purpose of this study was to investigate the effects of nutrient and macronutrient stress on complex variations in the phenolic profile and antioxidant status of Bellis perennis L. callus cultures. To obtain stress conditions, callus cultures were grown under insufficient nutrient conditions (different strengths of MS medium) or under conditions of limiting calcium (-Ca), magnesium (-Mg), or both (-Ca & -Mg). Phenolic content of callus cultures obtained from different stress treatments was detected quantitatively by LC-ESI-MS/MS analysis. The major compound was chlorogenic acid in all treatments. The accumulation of hesperidin, rutin hydrate, and chlorogenic acid was significantly induced by MS/2 while the highest quantity of caffeic acid was found in the MS/4 treatment. Nutrient and macronutrient stress resulted in a considerable increase in the activities of superoxide dismutase (SOD; EC 1.15.1.1) and catalase (CAT; EC 1.11.1.6), as well as in the content of proline, total phenolics, and flavonoids. The maximum increase of all antioxidants was obtained when calli were cultured on MS/2 medium. Our results revealed that different stress factors resulted in a complex variations in the phenolic profile with the induced antioxidant system, which could be associated with increased stress protection.