Background <p>This study was conducted to evaluate the elemental, micromorphological and microhardness changes in dentin after the removal of caries with sodium hypochlorite-based or enzyme-based chemomechanical caries removal (CMCR) agents.</p> Methods <p>Twenty-one cavitated carious molars and 7 noncarious permanent molars were used. The samples were split into four groups: group (1): traditional rotary technique; group (2): enzyme-based CMCR agent; group (3): NaOCl-based CMCR agent; and group (4): control (sound). After caries excavation, all the samples were subjected to elemental analysis via energy dispersive X-ray (EDX) spectroscopy, micromorphological analysis by scanning electron microscopy and, finally, Vickers microhardness testing. Elemental analysis results were evaluated via one-way ANOVA followed by Tukey’s HSD and Bonferroni post hoc comparisons. Vickers hardness values were analyzed via two-way ANOVA followed by Tukey’s HSD post hoc multiple comparison evaluations.</p> Results <p>Elemental analysis revealed no variation in Ca levels (<i>p</i> &gt; 0.05) among the four groups. The results revealed a variation (<i>p</i> &lt; 0.05) in P levels between the conventional rotary and control sound groups and the enzyme-based and NaOCl-based groups. The SEM results revealed occluded and partially occluded dentinal tubules and the presence of a smear layer following rotary caries removal and revealed patent dentinal tubules with minimal or absent smear layers following enzyme-based caries removal. Finally, there were patent dentinal tubules and a small smear layer following NaOCl-based caries removal. The Vickers hardness of sound dentin and remaining dentin after rotary caries removal was greater (<i>p</i> &lt; 0.05) than the Vickers hardness of the remaining dentin after CMCR by enzyme-based or NaOCl-based agents, and no variation (<i>p</i> &gt; 0.05) in the Vickers hardness of the remaining dentin was observed between the enzyme-based and NaOCl-based groups.</p> Conclusions <p>CMCR methods are conservative substitutes for rotary excavation and have translational potential for maintaining the repair capability of the dentin-pulp complex following clinical caries excavation. Compared with the NaOCl-based caries excavation technique, the Papain-based enzymatic CMCR agent appears to be a conservative substitute for traditional rotary excavation of carious tissue, and this enzymatic technique improved the morphological characteristics of the remaining dentin for further bonding. Unlike the conventional method and sound dentin, the mineral composition of dentin was affected by the two CMCR agents.</p>