Background: The potential of polyphenols to enhance the growth of beneficial intestinal bacteria through direct co-utilization by bacteria and their ability to inhibit pathogenic species is a topic of significant interest. Recently, the term "Duplibiotic" has been proposed to describe a non-absorbable substance that regulates the gastrointestinal microbiome through both antimicrobial and prebiotic mechanisms. Objectives: This study aimed to assess the prebiotic and antipathogenic effects of the aqueous extract of Cydonia oblonga Mill. Materials and Methods: This study examined the impact of an extract derived from C. oblonga Mill, a medicinal plant from the Rosaceae family, on the proliferation of Lactobacillus plantarum, Lactobacillus acidophilus, and Lactobacillus reuteri, as well as its antibacterial properties against six bacteria (enterohemorrhagic Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella enterica, Clostridium difficile, and Streptococcus mutans). Additionally, the minimum inhibitory concentration (MIC) of the C. oblonga Mill extract against these six bacteria was determined. Results: In general, various extract concentrations of the C. oblonga Mill were found to inhibit the growth of enterohemorrhagic E. coli, P. aeruginosa, S. aureus, C. difficile, and S. mutans, while significantly enhancing the growth of L. plantarum, L. reuteri, and L. acidophilus. Conclusion: The primary components of C. oblonga such as polyphenols may have a significant impact on biological properties. We suggest that the extract of C. oblonga Mill be considered a "Duplibiotic" compound, which refers to a non-absorbable substrate that modulates the gut microbiota through both antimicrobial and prebiotic mechanisms. The Duplibiotic effect of polyphenols is believed to contribute to reducing metabolic disorders and intestinal dysbiosis, positioning these compounds as nutritional interventions with medicinal capability.