Microorganisms like fungi, bacteria, and viruses are naturally present in different parts of a plant (root, bark, and leaf) and these become inhabitants of the plant. The establishment of modern Hazard Analysis and Critical Control Point (HACCP) approaches has therefore been made to evaluate the microbial load in medicinal plants. During the manufacturing of herbal extracts as drugs, the quality of the herbal extracts is dictated by the level of presence of microbes. In order to make the herbal extracts HACCP compliant as far as microbial load is concerned; we carried out studies with Glutaraldehyde (GA) as an antimicrobial agent in the manufacturing process in two randomly selected herbs of Salacia chinensis and Picrorhiza kurroa. The outcome of our analysis revealed that 0.5% of GA treatment to the pulverized raw material of Salacia chinensis and Picrorhiza kurroa is effective for reduction of > 99.99% microbial load with minimal effect on the percentage yield of extracts (10% - 20%) and their bioactive molecules Salacinol and Picroside I&II as seen by LC-MS and HPLC analysis, respectively. Furthermore, in this article, we demonstrate the use of sodium bisulfite for the removal of the residual GA in the extract to make the process eco-friendly and environment-safe.