Updated project metadata. Honey promotes health and is an effective non-pharmacological home remedy against common respiratory infections. However, industrial processing and manipulation of raw honey can have a detrimental effect on its biological activities, including antibacterial ones, and hence its health-benefiting qualities. Therefore, this study aimed to compare the honey’s antibacterial activity, its total protein content, and the abundance of the most dominant bee-derived proteins in honey between raw (n=92) and supermarket (n=17) samples. We showed that raw honey samples were much more effective in inhibiting the growth of Staphylococcus aureus with a median minimal inhibitory concentration (MIC) value of 4.5% compared to supermarket honey samples ceasing bacterial growth with a median MIC value of 36%. Moreover, raw honey samples contained significantly higher amounts of total protein as well as the content of particular bee-derived proteins (major royal jelly protein 1 (MRJP1), glucose oxidase (GOX), and α-glucosidase) in contrast to supermarket honey samples. These data hint that some marketed honey samples could be deliberately manipulated with syrup, especially those that exhibited low protein content. In addition, the supermarket honey sample with the lowest protein content contained α-amylase (diastase) from Aspergillus oryzae. Strikingly, the content of this foreign enzyme in honey was roughly 60 times higher than the naturally occurring bee α-amylase. Our findings highlight the burning need to refine and monitor the specific quality parameters, ensuring the authenticity of honey and maintaining its reputation as a functional food.