Background <p>This study aimed to evaluate the shear bond strength (SBS) of glass ionomer cement (GIC) modified with fluoride-loaded chitosan nanoparticles when applied to both sound dentin and caries-affected dentin (CAD).</p> Methods <p>Sixty human molar teeth were randomly allocated into two main groups based on dentin condition: sound dentin and CAD. Each group was further divided into three subgroups, containing 10 specimens each, as follows: conventional GIC, chitosan-modified GIC (CH-GIC), and fluoride-loaded chitosan nanoparticle-modified GIC (NCH-GIC). The occlusal surfaces of the teeth were ground to expose dentin, creating a 3 × 3&#xa0;mm dentin window. For subgroups 1, 2, and 3, the dentin surfaces remained untreated. In subgroups 4, 5, and 6, the dentin was subjected to a demineralization solution for 66&#xa0;h to simulate artificial carious lesions. Subsequently, the conventional and modified GICs were applied to the dentin surfaces, and SBS measurements were conducted. Statistical analysis was performed using one-way ANOVA, Tukey’s post hoc test, and Paired samples t-test.</p> Results <p>No significant differences in bond strength to sound dentin were found among the groups (<i>p</i> &gt; 0.05). However, bond strengths to CAD varied significantly (<i>p</i> &lt; 0.05) and the NCH-GIC showed notably higher SBS than conventional GIC (<i>p</i> &lt; 0.05). Conventional GIC had significantly lower shear bond to CAD compared to sound dentin (<i>p</i> &lt; 0.05) while the modified GICs showed no significant bond strength difference between the two dentin types (<i>p</i> &gt; 0.05).</p> Conclusions <p>Incorporating fluoride-loaded chitosan nanoparticles into glass ionomer cement significantly improved its bond strength to caries-affected dentin while maintaining comparable adhesion to sound dentin.</p>