Purpose: To evaluate how plant-based nanoparticles, specifically titanium, zirconium, and hydroxyapatite, influenced the wettability and surface roughness of glass ionomer cement (GIC). Materials and methods: The research involved 48 samples divided into four groups (n = 12 for each group)—GIC modified with green-mediated chitosan, titanium, zirconium, and hydroxyapatite (Ch-Ti-Zr-HAP) nanocomposite at concentrations of 3% (group I), 5% (group II), 10% (group III), and a control group of conventional GIC (group IV). Toothbrushing simulation was carried out using the ZM-3.8 SD Mechatronik toothbrush simulator with 30,000 brushing cycles. Atomic force microscopy (AFM), contact angle analysis, and scanning electron microscopy (SEM) were employed for nanoscale surface imaging, wettability assessment, and high-resolution surface examination, respectively. Statistical analysis included one-way analysis of variance (ANOVA), Tukey's post hoc analysis, and paired t-test. Results: The study revealed significant differences (p = 0.001) in contact angle values, with the 10 and 5% concentration groups showing the least contact angle postsimulation. Surface roughness analysis indicated that the 5% concentration group consistently had the lowest roughness parameters [arithmetic mean roughness (Ra), root mean square roughness (Rq), and average surface roughness (Sa)] (p = 0.001). SEM analysis illustrated that higher concentrations of nanomodifiers led to a denser and more uniformly distributed arrangement of nanoparticles on the GIC surface. Conclusion: Within the limitations of the study, green-mediated nanomodification of GIC with plant-based nanoparticles demonstrated promising outcomes in improving wettability and reducing surface roughness. The study highlights the potential of environmentally sustainable modifications to enhance the properties of dental restorative materials.