The secondary metabolism in medicinal plants are responsible for their protection against environmental factors and the health-promoting benefits they provide to users. The purpose of this study was to assess the responses of the secondary metabolic system of B. natalensis and its influence on the antioxidant and antibacterial activities. The phytochemical analyses, antioxidant and antibacterial assays were conducted from using harvested leaves, underground stems and roots from whole plants exposed to simultaneous elevated CO2 and temperatures over eight days in a heatwave simulation. Most of the phytochemical groups were present in the leaves, however majority of the tested compounds had consistent presence throughout the plants in all treatments. The underground stems possessed a greater total phenolic, tannin and proanthocyanidin contents than the leaves and roots under elevated CO2 and temperatures. The leaves had a comparatively better antioxidant activity from the treatment than control. Overall, there was consistency in the antibacterial activity in both control and experimental conditions. The tannins and phenolics had greater concentrations throughout the plants under elevated conditions overall, which could indicate their leading role in plant defence and the improvement and maintenance of the medicinal activity of B. natalensis. The responses of the plant parts of B. natalensis under elevated CO2 and temperatures provides newfound insights on the physiological roles plant organs play on the overall productivity and medicinal activity of the species.