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Although ethanolic-based propolis extracts have been shown to have various biological activities, studies on the differences in the antimicrobial effects of water- and ethanol-based extracts, are lacking. Propolis preparations are now also sold as water-based products due to a number of factors, such as being safer for babies, being biocompatible, and some religious prohibitions on alcohol consumption. This study aimed to compare the antimicrobial effects of commercially available propolis preparations in the form of ethanol- and water-based extracts against various pathogenic microorganisms that cause foodborne infections. A total of 36 Gram-positive and Gram-negative bacterial strains from 8 different species were used in the study. As a result of the statistical analysis, only ethanol-based propolis from Turkey was effective against enterococci, Staphylococcus aureus, Bacillus cereus, Bacillus subtilis subsp. spizizenii, Salmonella spp., Listeria monocytogenes, Acinetobacter baumannii, and Pseudomonas aeroginosa, except Escherichia coli. It was concluded that the water-based extract did not have a significant inhibitory effect on the bacteria tested. It was determined that both ethanol- and water-based propolis tested in the study showed the most inhibitory effect on Acinetobacter baumannii. In addition, we can also conclude that ethanol-based propolis extract is more effective against Gram-positive bacteria than Gram-negative bacteria.