This study aimed to assess the amount of erosion during activated endodontic irrigation with either HEDP or EDTA via high-resolution micro-computed tomography. Two root canals of twenty premolars were prepared with ProTaper Next and irrigated with sodium hypochlorite. Palatal canals, which served as control groups, were sealed, while buccal canals were further irrigated with either EDTA (n = 10) or HEDP (n = 10), which served as test groups. Micro-CT was performed to measure erosion depth. For 2D and 3D measurements, non-parametric repeated ANOVA measurements and post hoc tests were performed. 2D analysis showed highly significant differences between the case groups at each position of the root (p ≤ 0.01). The cervical and apical positions showed significant differences in the EDTA group (p = 0.03). The 3D analysis also showed significant differences between both chelating agents (p < 0.01) and the case and control groups (p = 0.01). The mean erosion depths in the cervical, middle, and apical thirds of the EDTA group were 45.75, 41.79, and 32.25 µm, and for the HEDP group were 20.25, 16.40, and 15.96 µm, respectively. HEDP seems to have a significantly less erosive effect. Different irrigation protocols with harsher conditions, as might be the case during endodontic retreatment, could be assessed with micro-CT.