Dental pulp and periapical diseases are common conditions in stomatology, caused by various pathogenic microorganisms. Antimicrobial peptides, as new antibiotics, offer promising applications in the irrigation and disinfection medicaments for root canals.One patient with chronic periapical periodontitis was selected to extract the clinical pathogenic bacteria. Porphyromonas gingivalis (Pg) (ATCC 33,277), Streptococcus mutans (Sm) (ATCC 25,175), and Prevotella intermedius (Pi) (ATCC 25,611) were used as test strains. The effects of plantaricin (Pln) 149 on the biofilm formation and growth in infected root canals were evaluated by RT-PCR, laser confocal scanning microscopy, and bacterial diversity analysis. In addition, the cytotoxicity of Pln 149 (100 µg/mL) to human dental pulp stem cells (hDPSCs) was assessed using an MTT assay. Pln 149 exhibited significant inhibitory effects on Pg Sm and Pi (P < 0.05), with significant differences in the biofilm images of the laser confocal scanning microscope (P < 0.05). There were no significant differences in hDPSCs viability or proliferation between the Pln 149 and control groups. Considering the excellent antimicrobial effects and low cytotoxicity, we suggest that Pln 149 might be a promising option for root canal irrigation solutions.