Introduction: Withania somnifera and Clitoria ternatea are commonly used herbs for the preparation of Ayurvedic products to treat most health problems. Objective: The present study was carried out to determine the Minimum Inhibitory Concentration (MIC) against microbes in stagnated rainwater. Methanolic extract of Withania somnifera root and Clitoria ternatea root were prepared and subjected to identification of the presence of alkaloids. Methods: Thin Layer Chromatography (TLC) method and the concentration was measured by UV spectrometry. Solvent extraction was carried out by maceration, orbital shaker and microwave oven methods. The extract was concentrated by the distillation process. The extract of W.somnifera collected from room temperature and the methanolic extract of C.ternatea was subjected to TLC method with the methanol as mobile phase. The compounds separated in the TLC plate was scraped off and subjected to UV spectrophotometry to identify the concentration of alkaloids present in the extract of both W.somnifera and C.ternatea. The extracts were tested for the anti-bacterial and anti-fungal activity. Results: The results found that the extraction of alkaloid compounds from W.somnifera can be enhanced by the microwaveassisted extraction and there was no change in the amount of extraction of alkaloids in C.ternatea. Finally, both the extract was subjected to anti-bacterial and anti-fungal activity. Different extracts from a single plant extracted by different extraction process show the different antimicrobial effect on microbes on stagnant rainwater. The type of extraction affects the anti-microbial effect of the extracts.