This study aimed at evaluating the mineral variation induced by polyalkenoate cements in residual dentine after different caries removal methods. Ten extracted sound molars were selected, and five cavities were prepared on the occlusal surface of each specimen. Carious lesions were generated using a microbial protocol, while the caries removal was performed using bur, hand excavator or two papain-based chemo-mechanical agents. One cavity was left unexcavated in each tooth. Cavities were restored using a zinc polycarboxylate cement (ZPC; n=25) or a glass ionomer was used (GIC; n=25). Subsequently, the specimens were stored under simulated pulpal pressure for 45 days. Micro-CT scanning was performed after caries formation, removal, and restoration. Cavity volumes (mm3) and mineral density (MD) changes were calculated. Remineralisation ability was investigated by scanning electron microscopy (SEM) and Fourier-transformed infrared spectroscopy (FTIR). Statistical analysis was performed (5% significance level). Baseline caries, cavity volume and MD increase after caries removal was similar for all excavation groups (p>0.05). MD was higher in ZPC compared to GIC (p<0.05). SEM revealed that the chemo-mechanical techniques produced a smoother dentine surface compared to mechanical methods. FTIR showed silicon-based minerals in GIC-treated dentine while ZPC-treated presented mineral deposits characterised by amorphous calcium phosphate. In both cases, the presence of carbonates was detected on dentine surfaces. All caries removal techniques performed similarly in terms of carious dentine excavation. ZPC can be used as dentine replacement material after caries removal as it may induce higher MD increase in residual dentine via deposition of calcium-phosphates, compared to GIC.