Pantoea vagans is an opportunistic pathogen for humans. This organism is frequently isolated from various horticultural commodities. Active compounds from some essential oils have been used to control food-borne pathogens. The objectives of this investigation were to determine the effect of four active constituents of essential oils on the morphological changes and membrane affectations of this microorganism. Scanning Electron Microscopy was used to observe morphological changes, while Fluorogenic techniques (LIVE/DEAD BacLight Kit, CFDA-SE, DiBAC4) were applied to evaluate membrane changes. The active compounds thymol, eugenol, carvacol and cinnamaldehyde altered and broke the bacterial membrane causing deformations and increase in permeability, a decrease in cytoplasmic pH (121.8 RFU, Relative Fluorescence Units) and depolarization (1841.025 URF). These active constituents could be an alternative for the control of P. vagans once they are tested in in situ studies.