The organism predominantly obtained from the oral biofilm was identified as Bacillus cereus which was observed to one of the root causes of pharyngeal infections. It was found that when the biofilm was treated with 16 * MIC (2.24 ± 0.12 µg/mL) there was an eradication of 62.78 ± 1.26% when treated with the ethanolic extract of Allium cepa as compared to 41.12 ± 0.98% when treated with antibiotic azithromycin. The in silico studies of identified bioactive compounds from the extracts depicting the synergism of the above two phytocompounds on the target biofilm-forming protein. The binding energy of synergistic interaction was found to be −33.521 kcal/mol, whereas antibiotic showed a value of −27.568 kcal/mol which in turn implied that through synergism a better antibiofilm activity could be obtained on B. cereus. It was observed that the viability of bacterial cells showed a marked reduction of 9.3% when challenged with 16 * MIC of ethanolic extract of A. cepa for a time period of 0–48 h with respect to control and standard antibiotic Azithromycin. The quantification of individual components of extracellular carbohydrates, proteins and nucleic acids showed maximum reduction in presence of ethanolic extract of A. cepa. Comparative quantification of the total concentration of bacterial genomic DNA and RNA showed maximum reduction in the presence of phytoextract. Thus this study clearly indicated by utilizing the synergistic properties of bioactive components of A. cepa, an effective substitute for conventional antibiotics can be developed which can be used for treatment against the biofilm-associated infections.