Berberis darwinii, known for its bioactive alkaloids like berberine and palmatine, has gained attention for its medicinal properties. However, comprehensive studies on the specific bioactive molecules of Michay are lacking, as previous research has primarily focused on wild plants. Therefore, this study proposes to evaluate the alkaloid content in various tissues of B. darwinii collected from different locations, aiming to identify high-yielding accessions suitable for consistent bioactive alkaloid production. This research focuses on plants from a cultivated Michay orchard established five years ago. Leaves, stems, roots, and fruits from 96 accessions of Michay were collected to obtain an alkaloidal extract used for the characterization and comprehensive analysis of bioactive alkaloids through high-performance liquid chromatography. Based on these results, a search for the main outliers was conducted to identify the accessions with the highest alkaloid production. The results showed that roots had the highest concentrations of both berberine and palmatine, followed by stems, while leaves and seeds had lower levels, and the pulp from fruits had no detectable alkaloids. Notably, alkaloid concentrations reached up to 30,806 mu g/g in roots, with accession C2P18 standing out for its combined total of 20,827.74 mu g/g of berberine and 9978.27 mu g/g of palmatine. Accession C3P26 showed the highest berberine concentration at 26,482.20 mu g/g. These values underscore the wide variation in alkaloid accumulation and highlight the potential for selecting elite accessions with exceptionally high yields. These findings highlight the importance of plant selection for optimal alkaloid extraction. Choosing high-yielding accessions and standardizing cultivation practices will ensure a stable supply of berberine and palmatine for pharmaceutical, nutraceutical, and food industry applications.