This study aimed to develop and characterize an experimental pulp-capping material incorporating collagen-hydroxyapatite nanocomposite (cHAP) derived from fish scales and chlorhexidine (CHX) as an antimicrobial agent. The synthesized cHAP was characterized using XRD, FT-IR, EDX, FE-SEM, and BET analyses. The nanocomposite and/or CHX were loaded onto a commercially available resin-based pulp-capping material (TheraCal LC). Experimental groups were defined as Control group, 1% cHAP (cHAP1), 5% cHAP (cHAP5), 5% chlorhexidine (CHX), and 2.5% CHX + 2.5% cHAP (cHAP-CHX). Standardized samples (6 mm diameter, 1 mm height) were prepared from experimental pulp-capping materials using a Teflon mold for subsequent analyses. Microhardness, monomer conversion, and antibacterial activity of the materials were investigated following SEM-EDX, XRD, and FT-IR analyses. Data were analyzed using one-way analysis of variance (ANOVA) and Tukey's post hoc test, with a significance level of p < 0.05. The cHAP and experimental pulp-capping materials were successfully characterized. CHX incorporation decreased microhardness significantly (p < 0.05), whereas cHAP-containing groups showed no significant differences compared to the control (p > 0.05). The degree of monomer conversion was unaffected by the addition of cHAP or CHX individually (p > 0.05), but a significant increase was observed when both CHX and cHAP were added (p < 0.05). Antibacterial testing revealed that E. faecalis was the most sensitive strain against the tested pulp-capping materials, with the cHAP-CHX group exhibiting the highest antimicrobial activity. The CHX and cHAP-CHX groups demonstrated antimicrobial activity against both E. faecalis and S. mutans, while the cHAP5 group was effective only against E. faecalis. The control group showed no antimicrobial activity against either strain. The addition of cHAP and CHX to the pulp-capping materials enhanced monomer conversion. Pulp-capping materials containing CHX and cHAP-CHX were particularly effective against E. faecalis and S. mutans. The integration of cHAP and CHX into the experimental resin-based pulp-capping materials offers a promising strategy for improving antibacterial activity and biocompatibility. This combination may serve as a potential candidate for enhancing pulp-capping procedures in clinical practice.