In the current study, both the essential oil composition and biological activity of Saussurea lappa and Ligusticum sinensis were investigated by means of microwave-assisted hydrodistillation (MAHD) and characterized by Gas chromatography/mass spectrometry (GC/MS), whereas the antimicrobial efficiency of MAHD essential oils was examined against four pathogens: Staphylococcus aureus, Escherichia coli, Aspergillus niger, and Candida albicans responsible for microbial infections. The goal was to spot synergy and a favorable method that gives essential oils to possibly use as alternatives to common antimicrobial agents for the treatment of bacterial infections using a microdilution assay. S. lappa's 21 compounds were characterized by MAHD extraction. Sesquiterpene lactones (39.7 % MAHD) represented the major components, followed by sesquiterpene dialdehyde (25.50 % MAHD), while L. sinensis's 14 compounds were identified by MAHD extraction. Tetrahydroisobenzofurans (72.94 % MAHD) was the predominant compound class. S. lappa essential oil collection showed the strongest antimicrobial activity with MIC values of 16 μg/ml against all pathogens tested, while L. sinensis showed strong antibacterial activity and moderate antifungal activity with MIC values of 32 μg/ml and 500 μg/ml, respectively. The principal components of both oils, (velleral, eremanthin and neocnidilide), were docked into the bacterial histidine kinase (HK) and the fungal heat shock protein 90 (Hsp90).