Objective: This study aimed to evaluate the efficacy of laser-activated irrigation using photon-induced photoacoustic streaming (PIPS®) and photoactivated disinfection (PAD) techniques and their combination to improve penetration and activation of toluidine blue in the endodontic space of teeth experimentally infected with Enterococcus faecalis. Materials and methods: Twenty-seven extracted single-root teeth were instrumented, sterilized, and infected with E. faecalis and divided into seven groups of three teeth each: Group A [sodium hypochlorite (NaClO) 5% hand irrigation], Group B [NaClO 5% hand irrigation+ethylenediaminetetraacetic acid (EDTA)+NaClO 5% activated by PIPS], Group C (EDTA+NaClO 5% activated by PIPS), Group D (toluidine blue activated by PAD), Group E (toluidine blue activated by PIPS and PAD), Group F (NaClO 5% hand irrigation+toluidine blue activated by PAD), and Group G (NaClO 5% hand irrigation+toluidine blue activated by PIPS and PAD). Finally, positive and negative group controls were prepared. The presence of biofilms after the treatments was assessed by the BioTimer assay. PIPS was performed with an Er:YAG laser (2940 nm, LightWalker, Fotona® d.o.o., Slovenia) at 20 mJ, 15 Hz, 0.3 W, and 50-μs pulse duration. PAD was performed with a 635 nm diode laser (Smart M, Lasotronix®, Poland) at 400 mW in continuous wave (CW). Results: When NaClO was used, significant decontamination (p ≤ 0.05) was obtained in all experimental groups with respect to the positive control, other than Group G. Irrigation with EDTA+NaClO activated by PIPS produced a higher level of decontamination than Group A (p ≤ 0.05). Significant results in reducing biofilm load compared with the control and Group A were observed when NaClO was coupled with toluidine blue activated by PAD (p ≤ 0.05). Conclusions: Disinfection of root canals can be obtained using a combination of different irrigants, photosensitizers, and activation protocols. EDTA+NaClO using the PIPS protocol and toluidine blue activated by PAD (both preceded by NaClO irrigation) can be considered effective tools. The possibility of replacing NaClO with toluidine blue, whatever the method of activation, should be further investigated.