Bacterial reinfection and root fracture are the main culprits related to root canal treatment failure. This study aimed to assess the utility of quercetin solution as an adjunctive endodontic irrigant that does not weaken root canal dentin with commitment anti-biofilm activity and bio-safety. Based on a noninvasive dentin infection model, dentin tubules infected with Enterococcus faecalis (E. faecalis) were irrigated with sterile water (control group), and 0, 1, 2, 4 wt% quercetin-containing ethanol solutions. Live and dead bacteria percentages in E. faecalis biofilms were analyzed by confocal laser scanning microscopy (CLSM). Elastic modulus, hydroxyproline release and X-ray photoelectron spectroscopy (XPS) characterization were tested to evaluate the irrigants' collagen-stabilizing effect. The cytotoxicity was tested by CCK-8 assay. Quercetin increased the proportion of dead bacteria volumes within E. faecalis and improved the flexural strength of dentin compared to control group (p < 0.05). Quercetin-treated dentin matrix had less elasticity loss and hydroxyproline release after collagenase degradation (p < 0.05). Moreover, quercetin solutions revealed an increase in the C-O peak area under both C1s and O1s narrow-scan spectra of XPS characterization, and no cytotoxicity (p > 0.05). Quercetin exhibited anti-biofilm activity, a collagen-stabilizing effect with cytocompatibility, supporting quercetin as a potential candidate for endodontic irrigant.