In this study, three potential probiotic strains were selected to ferment blueberry and blackberry juices. The viable cell counts of selected strains were increased by 0.4-0.7 log CFU/mL in berry juices environments after 48-h fermentation. Meanwhile, the contents of cyanindin-3-glucoside and peonidin-3-glucoside decreased over 30%. Heatmap presented an upgrade trend of syringic acid, ferulic acid, gallic acid and lactic acid during fermentation. However, the contents of p-coumaric acid, protocatechuic acid, chlorogenic acid, critic acid and malic acid showed downgrade trend. The metabolism of phenolics probably contributed to the enhancement of the ABTS radical scavenging activity (40%-60%) in fermented berry juices. Moreover, the three strains presented different capacities on changing the quality of berry juices according to the PCA and LDA analysis. The contents of individual organic acids had positive correlations with sensory quality, especially for sourness. Overall, probiotic fermentation could improve the sensory quality of berry juices.