Dracocephalum kotschyi essential oils obtained by hydrodistillation (HD), microwave-assisted hydrodistillation (MAHD), and solvent-free microwave extraction (SFME) were investigated by GC-FID (Gas Chromatography-Flame Ionization Detector) and GC-MS (Gas Chromatography-Mass Spectrometry). The percentage of oxygenated compounds was significantly increased from 62.52% in HD to 76.47% in MAHD, and 84.52% in SFME. Conversely, the monoterpene hydrocarbons were decreased from 30.84% in HD to 13.71% in MAHD, and 5.85% in SFME. The main compound in the essential oil obtained by HD is limonene, which accounted for more than 30% of the oil, while the percentage of this compound was reduced to 9.52% in MAHD, and 5.60% in SFME. The percents of other oxygenated compounds such as neral, geranial, geraniol, geranyl acetate, -terpineol, trans-verbenol, carvon, and trans-carveol were noticeably higher in microwave methods than those present in HD method. In aqueous medium, linear oxygenated monoterpenes may be converted to a monocyclic terpinyl cation, which it could lose a proton to give limonene. The main biosynthetic pathway of these compounds, as well as a possible route of their conversion into limonene, due to prolonged heating in the HD method, was proposed. The antimicrobial activity of D. kotschyi essential oils against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria was evaluated by broth micro-dilution susceptibility manner. The most sensitive bacteria to these oils was found to be S. aureus with the lowest minimum inhibitory concentration value of 2 mgmL(-1) for MAHD and SFME specimens. The results indicated that oils obtained by microwave methods were more active against S. aureus.