Smear layer removal from root canals aid in the penetration of both irrigants and endodontic sealer into the dentinal tubules, thereby improving the efficacy of endodontic treatment. The aim of this in vitro study was to compare the smear layer removal ability of a conventional endodontic irrigation regimen, MTAD (mixture of tetracycline, acid, and detergent), and QMix™ (Dentsply Sirona, Charlotte, North Carolina, United States) with that of a mixture of herbal irrigants, namely, aqueous extracts of Azadirachta indica (neem) and Citrus limon (lemon), evaluated using scanning electron microscopy (SEM). We selected 40 extracted human premolar teeth for the study, which we randomly divided into five groups (eight samples each) according to irrigation solution: (i) Group A (normal saline); (ii) Group B (conventional endodontic regimen, 3% sodium hypochlorite (NaOCl) + 17% ethylenediamine tetraacetic acid (EDTA) + 2% chlorhexidine (CHX)); (iii) Group C (MTAD); (iv) Group D (QMix 2-in-1); and (v) Group E (aqueous extracts of Azadirachta indica and Citrus limon). After we prepared the canals with ProTaper Universal nickel-titanium (Ni-Ti) rotary files (Dentsply Sirona) and the respective irrigants, we split the teeth longitudinally to evaluate the amount of remnant smear layer in the coronal, middle, and apical thirds using SEM photomicrographs. We performed statistical analyses of the data using the Kruskal-Wallis and Mann-Whitney U tests, where the level of significance was set at 0.05. The SEM analysis of the coronal third showed mean valuesof 3.83 in Group A, 3.67in Group B, 2.79in Group C, 3.63in Group D, and 4.00in Group E. The SEM analysis of the middle third showed mean values of 4.00 in Group A, 3.88in Group B, 3.75 in Group C, 3.50in Group D,and 3.50 in Group E.The SEM analysis of the apical third showed mean values of 3.92 in Group A, 3.63in Group B, 3.71in Group C, 3.88 in Group D, and 3.17 in Group E.Therefore, we found that there were significant statistical differences between the groups when an overall comparison was done for the coronal, middle, and apical third, with a p-value of 0.001. On multiple comparisons across the different tooth-section thirds. Groups A and B showed statistically significant differences in the apical third (p-value=0.017). Groups A and C showed statistically significant differences in the coronal third and middle third (p-values=0.001 and 0.010, respectively). Groups A and D showed statistically significant differences in the middle third (p-value=0.001). Groups A and E showed statistically significant differences in all thirds (p-values=0.039, 0.001, and 0.001, respectively) Conclusion: The conventional needle irrigation with MTAD showed the highest level of smear layer removal ability on the root canal surface, followed by QMix 2-in-1, the Azadirachta indica leaf and Citrus limon extract mixture, and the conventional endodontic regimen. Normal saline showed the lowest smear layer removal effect.