This work is aimed at the development of a microcolumn HPLC-UV assay for the rapid quantitative analysis of arbutin, bergenin, and gallic acid in Bergenia crassifolia. The results obtained indicate appropriate metrological parameters of the developed assay. It was found that the known methods of quantitative analysis of phenolic glycosides using SPE-spectrophotometry cannot be characterized as selective and accurate, due to the fact that the presences of the impurity compounds that do not belong to the group of phenolic glycosides negatively influenced the results. The developed assay was used for quantitative analysis of wild and commercial samples of B. crassifolia raw material. It was found that the content of arbutin, bergenin, and gallic acid in samples of B. crassifolia rhizomes collected in the Republic of Buryatia was 38.58–45.97, 66.74–139.76 and 1.22–1.65 mg/g, respectively, and for commercial batches of raw materials 20.57–41.37, 35.04–83.94 and 0.22–1.28 mg/g, respectively. It was found that the process of gradual enzymatic changes in the color of B. crassifolia leaves (green, red, black) leads to significant changes in the chemical composition. The most pronounced phenomenon is the degradation of bergenin, the presence of which is noted only in green leaves. The concentration of gallic acid is reduced in black leaves. Arbutin is characterized by an increased content in red leaves (102.02 mg/g). Additionally, a quantitative analysis of the peduncles and flowers of B. crassifolia was realized, and it was shown that they are distinguished by a high content of arbutin 48.40 and 42.15 mg/g, respectively, as well as bergenin in flowers (16.89 mg/g). The study demonstrated that the developed technique can be applied for a quick, selective, and accurate quantitative analysis of three compounds in various organs of B. crassifolia.