Berberrubine is primarily studied for its biological activity, particularly in the field of pharmacology and natural product research. It exhibits significant antimicrobial properties, showing effectiveness against various bacteria and fungi, making it a candidate for development in anti-infective agents. It also demonstrates anti-inflammatory and antioxidant effects, which are valuable in managing oxidative stress-related conditions and chronic inflammation.

Research indicates berberrubine has potential anticancer activity by interfering with cell proliferation and inducing apoptosis in certain cancer cell lines. Its ability to modulate key cellular signaling pathways supports its investigation in oncology. Additionally, it has been explored for its antidiabetic effects, where it may help in improving insulin sensitivity and glucose metabolism.

Due to its structural similarity to other isoquinoline alkaloids, berberrubine is also used as an intermediate in the synthesis of more complex bioactive molecules. Its natural origin and low toxicity profile enhance its appeal for use in traditional medicine and as a lead compound in drug discovery.