Elettaria cardamomum is cultivated in the Southern part of India showed great extinct of differences in their morphotypes and chemical compositions. In the present study, we have selected three varieties of Elettaria cardamomum “Valley Green, Palakuzhi, and ICRI”, to analyze the morphological perturbations, chemical compositions, and antimicrobial activities. The differences in the morphological character of cardamom varieties (Valley Green, Palakuzhi, and ICRI) were carried out on the basis of panicles, capsules shape, plant height, tiller, and seeds per capsule. The GC-MS analysis of the essential oils resulted in the identification of 27, 29, 30 compounds representing over 97.4%, 95.2%, and 98.8% of the Valley Green (VG), Palakuzhi (PAL), and ICRI fruit oils respectively. Monoterpene, α-terpinyl acetate varied from 35.4 to 47.5%, a major constituent while 1,8-cineole (22.8% to 27.4%) observed the second major compounds revealed in oils of these cultivars. Further, the antimicrobial activities of each essential oils were performed against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Klebsiella pneumoniae, Candida albicans, and Aspergillus niger. The maximum inhibition percentage against the microbes was observed in Valley Green essential oil as compared to oils of other varieties.