The present study aims to investigate the preliminary phytochemical screening and various separation techniques to isolate the bioactive compounds from the endophytes of Datura metel. The ethyl acetate extracts of the endophytes are used for the current study. Phytochemical screening of the extracts revealed the presence of tannins, alkaloids, terpenoids and tropane alkaloids. The quantitative amounts of tropane alkaloids are significant in actinomycete (29.4%) than the endophytic fungus (23.2%). Actinomycete seems to contain higher phenolic content of 1. 271 mg/g whereas endophytic fungus accounts only 1.254 mg/g. The IR spectroscopic studies of endophytic fungus and actinomycetes showed peaks at different points and the results are noted. Hence, the isolation and production of bioactive compounds from the endophytes may facilitate the new product discovery process.