Essential oils are promising antimicrobial agents against various bacteria. The aim of the study was to examine anti-Acinetobacter baumannii activity of nine essential oils and to elucidate essential oil mechanisms of action against this. In total, 8 out of 9 examined different essential oils exhibited activity against multidrug-resistant (MDR) A. baumannii isolates. The best anti-A. baumannii activity expressed Thymus serpyllum, Satureja hortensis and Oreganum majorana essential oil (MBC 1.29 to 2.58 µg mL−1), while essential oils of Menta x piperita, Hyssopus officinalis, Foeniculum vulgare and Artemisia dracunculus expressed the same effect in higher concentrations (1.80 to 3.80 µg mL−1). The effect of Juniperus sabina, Juniperus sibirica and S. hortensis essential oils against A. baumannii is for the first time reported here. The mechanisms of Myrtus communis, Eucalyptus camaldulensis, S. hortensis and T. serpyllum essential oils were further examined. The essential oil treatments led to concentration dependent leakage of biomolecules form the cells, causing an increase in the concentrations of lipids, carbohydrates, and proteins in the suspensions. Microstructural observations confirmed the essential oil effect on cell membranes and disruption the membrane integrity, with obvious leakage of intercellular substance, collapsed cells with perforations, debris presence and autoaggregated cells. The subinhibitory concentrations of oils did not obviously changed protein patterns determined by SDS-PAGE. These results indicate that the essential oils, particularly T. serpyllum, S. hortensis, M. communis and E. camaldulensis express its anti-A. baumannii activity via membrane disruption and increased membrane permeability, representing very promising alternative antibacterial agents against MDR wound isolates.