Objective: This scoping review aimed to map and summarize the evidence on the antimicrobial and antibiofilm efficacy of flavonoid-based solutions or formulations for endodontic applications. Design: The review was conducted in accordance with the PRISMA-ScR guidelines. A comprehensive search was performed across databases for articles published up to April 2025. Eligible studies included those evaluating the antimicrobial effects of flavonoids on microorganisms associated with endodontic infections. Relevant data were extracted, and a descriptive synthesis of the findings was carried out. Results: The results showed that fifteen studies met the inclusion criteria, demonstrating significant antimicrobial and antibiofilm activity of various flavonoids. Epigallocatechin-3-gallate was the most extensively studied compound, showing dose-dependent activity against E. faecalis, F. nucleatum, A. israelii, S. mutans, and C. albicans, with enhanced efficacy when combined with agents such as fosfomycin or the peptide KR-12-a5. Quercetin also displayed concentration-dependent antibiofilm effects and gene modulation in E. faecalis. Proanthocyanidin showed superior efficacy compared to conventional irrigants, especially at higher concentrations. Rutin, although limited in standalone efficacy, showed promising results when used as a photosensitizer. Other flavonoids such as apigenin, theaflavin, isoquercitrin, ampelopsin, chalcone, and chrysin also demonstrated varying degrees of antimicrobial activity, often similar to or surpassing conventional agents like chlorhexidine and calcium hydroxide in specific models. Conclusions: Flavonoids exhibit significant potential as alternative or adjunctive agents for endodontic disinfection, especially in biofilm-related infections. Their efficacy is influenced by compound type, concentration, formulation, and synergistic combinations. Further research, especially clinical trials, is warranted to validate their therapeutic applicability and optimize delivery systems for clinical use in endodontics.