In recent years, an increasing interest in phytotherapy has been observed. Parallel to the research on the total extracts of plant material, numerous studies on the activity of single molecules derived from plants are being conducted to address their mechanisms of action and determine active doses and eventual interactions. Despite this phenomenon, the isolation of individual compounds is a bottleneck due to its difficulty and cost. This work presents the results of a careful optimization of magnoflorine and berberine (isoquinoline alkaloids) recovery from a commonly distributed shrub, Berberis vulgaris, growing in Poland and Georgia, using CPC. Both compounds are known for their numerous medicinal properties, which makes the isolation methodology an important area of research. Additionally, CPC has the ability to isolate high-quality compounds in large quantities, which makes it an effective and easy-to-commercialize method. For a successful separation, the biphasic solvent system composed of hexane, butanol, ethanol, and water in a ratio (3:12:4:16 v/v/v/v) was used in the ascending mode, together with the flow rate of 8 mL/min and rotation speed of 1600 rpm. The method was selective for both compounds, and it delivered good results for both root and stem extracts from the plant. The qualitative composition of alkaloids in the studied extracts determined by HPLC-ESI-QTOF-MS/MS confirmed the presence of berberine, magnoflorine, jatrorhizine, and palmatine alkaloids from the group of isoquinolines. The isolates, magnoflorine and berberine, were subjected to the Helicobacter pylori growth inhibition assay and urease inhibition test to assess whether, next to the previously proved anticancer properties, these compounds are characterized by H. pylori inhibition. MGN was found to exhibit inhibitory potential against urease (IC50 = 25 mg/L). Keywords: magnoflorine; berberine; alkaloids; centrifugal partition chromatography; Berberis vulgaris; natural substance; extraction