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The escalating global challenge of antimicrobial resistance has driven significant interest in exploring natural, plant-based alternatives with bioactive properties. Fruit vinegars, long valued in traditional wellness practices for their purported health benefits, represent a promising category of such functional foods. However, the specific phytochemical profiles and antimicrobial efficacy of vinegars derived from underutilized fruits, particularly Phoenix dactylifera (date) and Musa paradisiaca (banana), are not well-documented. This study was therefore designed to characterize the phytochemical composition and evaluate the in vitro antimicrobial potential of vinegars produced from these fruits. Yeast (Saccharomyces cerevisiae strain SR 128) and acetic acid bacteria (Acetobacter aceti strain WI) were isolated from spoiled fruits and used to inoculate musts for submerged fermentation. The resulting vinegars were analyzed for their physicochemical properties, nutrient content, and phytochemical constituents using established gravimetric and instrumental methods. Antimicrobial activity was assessed against a panel of pathogenic microorganisms, including Staphylococcus aureus, Escherichia coli, Salmonella enterica serovar Typhi, and Candida albicans. Statistical analysis was performed using ANOVA followed by Tukey’s post-hoc test (p < 0.05). Phytochemical analysis confirmed the presence of bioactive compounds, including alkaloids, saponins, flavonoids, tannins, and cardiac glycosides. Both vinegar samples exhibited significant (p < 0.05) inhibitory activity against all tested pathogens, with the most pronounced effect observed against E. coli. Comparative analysis indicated that the date fruit vinegar possessed marginally superior antimicrobial efficacy. In conclusion, this study demonstrates that vinegars from Phoenix dactylifera and Musa paradisiaca are rich sources of antimicrobial phytochemicals, and the sample produced from PD was slightly better than the sample produced from MP, mostly against Escherichia coli.