Berberis integerrima Bunge is a valuable plant of the Berberidaceae family used in medicine and industry. The properties of the different parts of this plant vary and depend on the distribution of its secondary metabolites, including alkaloids and phenolic compounds. Here, we aimed to evaluate and compare phenolics and alkaloids of the different organs and tissues of B. integerrima. Our results showed that the highest content of phenolic compounds was found in the fruit and leaf, while the total alkaloid level was higher in the root. In the fruit, leaf and stem, the main phenolic acids were caffeic acid, cinnamic acid and gallic acid, respectively. In contrast, the highest levels of ferulic acid, catechin, resveratrol and luteolin were detected in the root. The highest content of berberine, one of the most important alkaloids of barberry, was found in the root, especially in the bark tissue. Further experiments showed that phenolic compounds and berberine, in the aerial organs and root of B. integerrima, respectively, are likely responsible for the antioxidant capacity of these organs. Given the high berberine content of the root (6.26 mg g-1 Dry Weight), and after trying to find a simple yet effective method to extract berberine, it was found that 80% ethanol containing 2% acetic acid at 25 °C with 72 h of maceration gave the highest berberine yield. Overall, the distribution and accumulation patterns of the secondary metabolites in the different organs of B. integerrima lead to their different applications.