Numerous studies have explored the antibacterial properties of different types of honey from all around the world. However, the data available describing how honey acts against bacteria are few. The aim of this study was to apply a flow cytometry (FC) protocol to examine and characterize the primary effects of three varieties of honey (avocado, chestnut and polyfloral) upon physiological status of Staphylococcus aureus and Escherichia coli cells to reveal their antibacterial action mechanisms. The effects of honey samples on membrane potential, membrane integrity, and metabolic activity were assessed using different fluorochromes, in a 180 min time course assay. Time-kill experiments were also carried out under similar conditions. Exposure of S. aureus and E. coli to the distinct honey samples resulted in physiological changes related to membrane polarization and membrane integrity. Moreover, honey induced a remarkable metabolic disruption as primary physiological effect upon S. aureus. The different honey samples induced quite similar effects on both bacteria. However, the depth of bacteria response throughout the treatment varied depending on the concentration tested and among honey varieties, probably due to compositional differences in the honey.