Background: Treating tooth root canal systems with Er:YAG laser together with irrigants has been shown to be effective in reducing biofilms formed by Enterococcus faecalis. This study investigated whether laser-activated irrigation (LAI) with side-firing Endo tip (LiteTouch™; Light Instruments, Yokneam, Israel) affects dentin mineral composition when used with common endodontic irrigants. Methods: Root canals of extracted human teeth were treated with Er:YAG laser using a side-firing Endo tip combined with 17% ethylenediaminetetraacetic acid (EDTA) and/or 2.5% NaOCl in continuous or intermittent mode for 60 s. Dentin mineral composition (Ca, P, O) in coronal, middle, and apical regions of root canals was examined by energy dispersive X-ray spectroscopy. Results: The use of LAI with continuous EDTA resulted in the largest reduction in Ca and P levels. A final NaOCl rinse mitigated the EDTA-mediated mineral loss in all root canal regions and increased the O content. Likewise, the reduced Ca/O and Ca/P ratios caused by continuous EDTA irrigation were reversed when combined with a final NaOCl rinse. Conclusions: LAI with Er:YAG Endo tip using continuous EDTA irrigation followed by NaOCl caused minimal dentin mineral loss and can therefore be considered to be a safe treatment module for cleaning root canals.