The purpose of this study was to compare the penetration of methylene blue (MB) dye after laser irradiation using PIPS (photon-induced photoacoustic streaming) and SWEEPS (shockwave enhanced emission photoacoustic streaming) methods compared to Passive ultrasonic irrigation (PUI) and to study their effect on dentin microhardness. A total of 44 single-rooted human teeth which were extracted for orthodontic or periodontal reasons were used. The teeth were decapitated to standardize roots to 12 mm in length. Canals were prepared up to size #30.6% and divided randomly into four groups (n = 11/group) according to the method of NaOCl activation: Group I: Er: YAG laser activation with PIPS tip; Group II: Er: YAG laser activation with SWEEPS tip; Group III: passive ultrasonic irrigation (PUI) and Group IV: conventional needle irrigation (CI). MB dye was injected then teeth were sectioned horizontally into coronal, middle and apical sections. Penetration depth/area percentages were measured using stereomicroscopy. Coronal specimens were further subjected to Vickers microhardness testing. Data were statistically analyzed. SWEEPS and PIPS activation methods provided higher dye penetration depth and area percentages compared to PUI with no statistically significant differences between all test groups. However, all test groups showed statistically significant differences with the CI (control) group. SWEEPS activation provided higher microhardness values with statistically significant differences with the other groups. Laser irrigant activation using PIPS and SWEEPS is comparable to PUI concerning MB dye penetration. However, SWEEPS preserved dentin microhardness significantly which can be beneficial for the long-term prognosis of root canal treated teeth.