Foodborne pathogens are a serious threat to human health when they contaminate food products. Nowadays, consumers are interested in natural, safe, multi-health benefits food and at the same time increasingly concerned about food chemical preservatives and additives. Due to this fact, it is important to focus on natural alternatives for food products preservation. Data related to antimicrobial properties of cranberry fruit are available; however, information regarding morphostructural damage due to foodborne pathogens, due to the natural extracts is still scarce. This study was performed to evaluate the morphostructural effects of swamp cranberry water–ethanol pomace extract (WEPE) on selected Gram-positive (Staphylococcus aureus and Listeria monocytogenes) and Gram-negative (Escherichia coli and Salmonella Enteritidis) foodborne bacterial pathogens. The morphological and ultrastructural alterations of extract-treated bacteria cells were observed using transmission electron microscopy technique (TEM). In our study, TEM revealed changes in the cell structure and the integrity of cells both for Gram-positive and Gram-negative strains. Our investigation revealed substantial structural damage at the cellular level and irreversible cell membrane rupture with the apparent leakage of intracellular contents. Present results indicate that WEPE is highly effective against foodborne pathogens, so as the antimicrobial effect of WEPE, including destructive influence on bacterial cells proved in this study, suggests promising potential use of cranberry extract as a natural preservative in food products. Influence of WEPE on other processes, such as inhibition of nucleic acid synthesis, inhibition of cell wall and membrane protein synthesis or disturbance of cellular energy metabolism, should be the subject of further research.