This study shows the changes in physicochemical and microbiological composition, and in the phenolic profile of black tea kombucha during fermentation. In addition, the antimalarial potential of the kombucha was evaluated. Ultra-performance liquid chromatography-mass spectrometry multiplex analysis (UPLC-MSE) results revealed a 1.7 log2 fold-change increase in phenolics with the fermentation time, with emphasis on the increase of phenolic acids (0.3 log2 fold-change). Over time there was degradation of flavonoids such as nepetin, hesperidin and catechin 5-O-gallate, to the detriment of the increase in phenolic acids such as gallic acid and cinnamic acid. In addition, black tea kombucha presented antiplasmodic activity against the 3D7 (sensitive chloroquine) and W2 (resistant to chloroquine) strains. Therefore, important changes in the black tea kombucha phenolic profile take place during fermentation, which may help in the development of kombuchas with higher bioactive potential and contribute to a better understanding of the kombucha fermentation process.