Replacing the conventional endodontic irrigants with herbal agents could avoid complications associated with using sodium hypochlorite (NaOCl). Endodontic irrigants alter the surface roughness of the dentinal wall surface, which affects sealer mechanical retention. This study aimed to assess the effect of experimental herbal Moringa oleifera and orange peel extract irrigant on intraradicular dentin (IRD) surface roughness using quantitative 3D surface analysis by scanning electron microscopy (SEM) regarding the smear layer assessment. Sixty human root sections were divided into four groups (n = 15): NaOCl combined with 17% ethylenediaminetetraacetic acid (EDTA); negative control (saline); moringa extract (MO); and orange oil (OO). SEM images were assessed quantitatively for surface roughness (Ra) in the coronal, middle, and apical IRD. The data were analysed by Kruskal–Wallis, Friedman, and Dunn’s tests. All groups showed statistically significant differences (P = 0.007). MO exhibited significantly greater Ra values at the coronal, middle, and apical root levels than OO (P = 0.007, 0.009, and 0.046, respectively). There was no significant change in Ra values at various root levels within each group at P = 0.091, 0.819, 0.819, and 0.549 for the EDTA, saline, MO, and OO groups. Considerable (IRD) surface roughness analysis makes Moringa extract a promising herbal endodontic irrigant alternative to the NaOCl plus EDTA regimen.