The current study evaluated the antibacterial properties of industrial sweet orange waste extracts (ISOWEs), which are a rich source of flavonoids. The ISOWEs exhibited antibacterial activity towards the dental cariogenic pathogensStreptococcus mutansandLactobacillus caseiwith 13.0 ± 2.0 and 20.0 ± 2.0 mg/mL for MIC (minimum inhibitory concentration) and 37.7 ± 1.5 and 43.3 ± 2.1 mg/mL for MBC (minimum bactericidal concentration), respectively. When evaluated in a 7-day dual-species oral biofilm model, ISOWEs dose-dependently reduced the viable bacteria count, and demonstrated strong synergistic effects when combined with the anti-septic chlorhexidine (at 0.1 and 0.2%). Similarly, confocal microscopy confirmed the anti-cariogenic properties of ISOWEs, alone and in combination with chlorhexidine. The citrus flavonoids contributed differently to these effects, with the flavones (nobiletin, tangeretin and sinensetin) demonstrating significantly lower MICs and MBCs compared to the flavanones hesperidin and narirutin. In conclusion, our study demonstrated the potential of citrus waste as a currently underutilised source of flavonoids for antimicrobial applications, such as in dental health.