Objective To investigate an intracanal disinfection methodology of APNPs (atmosphere pressure nonequilibrium plasmas) or modified APNPs in root canal treatment and evaluate the antimicrobial efficiency against in vitro infected dentinal tubules and in vivo experimental apical periodontitis. Materials and methods Dentine specimens were centrifugated with Enterococcus faecalis to generate 1-day-old and 3-week-old biofilms, and were treated with 2% chlorhexidine (Chx), APNP or modified APNP for 3 and 10 min (n=4). LIVE/DEAD staining was employed to analyze the ratio of deactivated bacteria. Experimental apical periodontitis in beagles was induced. Root canal therapy with APNPs or modified APNPs was performed and the antimicrobial effect was evaluated by histological and radiographical analyses. Results APNP deactivated 1-day-old and 3-week-old E. feacalis in dentinal tubules as much as 2% Chx irrigating. Modified APNP significantly deactivated more E. faecalis biofilms in dentinal tubules for 3-min and 10-min treatments, without thermal damage or dentinal destruction being observed. In beagles' apical periodontitis, significantly increased BV/TV and decreased lesion volume of apical bone were found in modified APNP group than 2% Chx irrigation group according to mu CT. Fewer inflammatory cells and bacterial residual in dentine were observed in modified APNP-treated apical tissue by histology staining compared with those in the 2% Chx irrigation group. Conclusion The antimicrobial effect of APNP jet irradiation was comparable to that of 2% Chx irrigation. No structural damage in dentine or tissue necrosis at the periapical region was induced upon treatment. The modified APNP demonstrated an increased antimicrobial efficacy compared with 2% Chx irrigation both in vitro and in vivo.