The aim of the study was to evaluate the influence of 17% ethylenediaminetetraacetic acid (EDTA) and ethanolic extract of Sapindus mukorossi (S. mukorossi) in combination with canal shaping on surface properties of ProTaper Gold rotary endodontic file. Sixteen F1 ProTaper Gold rotary files underwent the standard protocol for root canal treatment using two irrigants (S. mukorossi and 17% EDTA) in single-rooted decoronated teeth. Eight unused files were used as a control. All files were examined under an atomic force microscope (AFM) to evaluate surface roughness (Ra) and root mean square (RMS). Data were analyzed using the t-test. RMS and Ra values of the control file were 1.37 and 0.607, respectively. The mean RMS (3.70 ± 1.41) and mean Ra (2.89 ± 1.41) in EDTA group were significantly higher than the control file (p < 0.05). The mean RMS in the S. mukorossi group (1.77 ± 0.66) did not show any significant difference with the control (p > 0.05). The Ra of S. mukorossi group (1.09 ± 0.05) was significantly higher than the control file (p < 0.05). Moreover, the mean RMS and Ra were found to be significantly higher in the EDTA group compared to the S. mukorossi group (p < 0.05). The mean Ra and RMS values of the ProTaper Gold files used to prepare canals using 17% EDTA and S. mukorossi irrigation were significantly higher than the control files. The EDTA-treated ProTaper Gold rotary files demonstrated higher surface Ra and RMS than the S. mukorossi files.