C. fenestratum stem samples are extensively harvested from the wild for the extraction of an important anti-diabetic drug berberine as well as for the crude ayurvedic formulations. Whole plants are uprooted as a source of berberine. Since the main source of berberine is the stem, a comparative assessment has been undertaken to study the variation of berberine content upon subjecting it to different combinations of drying and extraction procedures. The extracts were analyzed by high performance liquid chromatography (HPLC). Method of extraction and method of drying significantly influenced the berberine yield in C fenestratum. Methanol cold extraction is the best and efficient method for the highest product recovery. Highest yield of berberine (4.06 % w/w) was obtained in the shade dried samples followed by the sundried samples (3.21% w/w) extracted with cold methanol.