Successful root canal treatment requires effective irrigation of the entire root canal system. While chelating agents support irrigation, they can also alter physicochemical properties of the root dentin structure. The aim of this study is to evaluate the effect of different chelation agents on root dentin roughness. Twenty‐five extracted maxillary incisors were used in this study. Samples were separated longitudinally and divided into five groups: distilled water, NaOCl, ethylenediaminetetraacetic acid (EDTA), phytic acid and citric acid (CA). Atomic force microscope and energy dispersive X‐ray spectroscopy analyses were used for analysing. One‐way analysis of variance and Turkey tests were used in the statistical analysis of the study. EDTA, CA and phytic acid solutions increased the roughness and phytic acid and CA solutions decreased the Ca/P ratio in dentin tissue. No statistical difference was observed in the other groups. The decrease of Ca/P ratio should be taken under consideration during irrigation. The increase in surface roughness may provide clinical benefit by supporting the adhesion of the root canal filling materials to the dentin surface.