This in vitro study compared the antimicrobial efficacy of 2.5% sodium hypochlorite (NaOCl) and 8 µg/mL ozonated water agitated by passive ultrasonic irrigation (PUI) or PUI combined with EndoActivator (EA) against mature multispecies biofilm. One hundred and five oval-shaped mandibular premolars were instrumented, sterilized, and inoculated with Enterococcus faecalis, Candida albicans, and Staphylococcus aureus, divided into: control group - saline; O3 group - ozonated water; O3 PUI group - ozonated water with PUI agitation; O3 PUI+EA group - ozonated water with PUI+EA agitation; NaOCl group - NaOCl; NaOCl PUI group - NaOCl with PUI agitation; and NaOCl PUI+EA group - NaOCl with PUI+EA agitation. Microbiological samples were collected before (S1) and after (S2) the disinfection procedures and the data were statistically analyzed using the Kruskal-Wallis test. In the culture method, there was significant disinfection in the O3 PUI+EA, NaOCl, NaOCl PUI, and NaOCl PUI+EA groups (p˂0.05). The combination of NaOCl with PUI+EA reduced microbial counts to zero (p˂0.05). In the qPCR method, there was a significant reduction in the total count of viable microorganisms in the O3 PUI, O3 PUI+EA, NaOCl, NaOCl PUI, and NaOCl PUI+EA groups (p˂0.05). It can be concluded that 2.5% NaOCl with and without agitation, as well as 8 µg/mL ozonated water with its action enhanced by the agitation techniques, were effective in root canal disinfection, and their antimicrobial efficacy is related to the microorganisms present in the biofilm.