Solvent‐free microwave extraction (SFME) and microwave‐assisted hydrodistillation (MAHD) were utilized for extraction of lemon verbena essential oil (EO) in comparison with the conventional hydrodistillation (HD). Chemical composition, extraction yield, physical properties, operation cost, antioxidant activity, and antifungal activities of extracted EOs were measured. Final yields of extraction and physical properties of extracted EOs did not show any significant difference among the three methods, but the required extraction time for extraction by microwave‐assisted extraction (MAE; i.e., MAHD and SFME) methods improved to a shorter time span. Even though the compounds in all three extraction techniques were exactly similar, extraction by MAE methods, especially the SFME, increased the quantity of oxygenated compounds such as citral isomers (geranial and neral) in comparison with HD. The obtained results showed that MAE methods, especially SFME, can selectively extract oxygenated compounds such as citral isomers and improve antioxidant and antifungal activities of the extracted EOs. Practical applications Oxygenated compounds like citral isomers are mostly effective in treating many health disorders. According to the results of this study, microwave extraction like MAHD and SFME result in the enrichment of citral isomers of EOs. This selective extraction can affect antioxidant and antifungal activities of EOs extracted by the microwave method in comparison with conventional methods like HD.