This study investigated the impact of Lactobacillus acidophilus NCFM, Oenococcus oeni Viniflora® Oenos and Lactobacillus brevis CICC 6239 on bog bilberry juice with a considerably low pH and rich in anthocyanins content. Moreover, the effects of the strains on the composition of phenolic compounds, amino acids, ammonium ion, biogenic amines, reduced sugars, organic acids, and color parameters of the juice were studied. All three bacteria consumed sugars and amino acids but exhibited different growth patterns. Lactic acid was detected only in L. acidophilus inoculated juice. The content of the phenolic compounds, especially anthocyanins, decreased in juice after inoculation. The CIELa*b* analysis indicated that the juice inoculated with L. acidophilus and O. oeni showed a decrease on a* and b* (less red and yellow) but an increase on L (more lightness), whereas the color attributes of L. brevis inoculated juice did not significantly change. Based on this study, L. brevis showed the most optimal performance in the juice due to its better adaptability and fewer effects on the appearance of juice. This study provided a useful reference on the metabolism of lactic acid bacteria in low pH juice and the evolution of primary and secondary nutrients in juice after inoculated with lactic acid bacteria.