Aim: The study aimed to evaluate the effect of bacterial cellulose nanocrystals (BCNC) addition on the mechanical, morphological, and optical properties of zirconomer. Materials and methods: Zirconomer with varying amounts of BCNCs (0.2, 0.5, and 1.0%) was then prepared. The mechanical properties of the specimens were tested for compressive strength (CS) and flexural strength (FS) using a universal testing machine. Meanwhile, scanning electron microscopy–energy dispersive X-ray (SEM-EDX) and Fourier transform infrared (FTIR) spectroscopy were performed to characterize the sample. The L*a*b* values were measured against a black-and-white background using a spectrophotometer to analyze the color mean difference. Results: Generally, the incorporation of BCNCs in the zirconomer matrix did not significantly improve the mechanical properties of the composite. However, the addition of a small amount of BCNCs (0.2%) in the glass ionomer cement (GIC) led to significant improvements (p < 0.05) in the compressive strength (+1.4x compared with the control group) but did not significantly change the flexural strength. BCNCs are evenly distributed in the sample SEM image, which may explain the enhancement of certain mechanical properties of the sample. In fact, a rougher and more heterogeneous texture on the sample surface was observed as BCNCs increased. FTIR confirms bonding or close association between the zirconium species and the BCNC matrix. The 0.2% BCNCs sample had relatively better color stability (p > 0.05) compared to the control. Conclusion: The findings suggest that incorporating a small amount (0.2%) of BCNCs into zirconomer could enhance its mechanical properties, particularly compressive strength, while maintaining acceptable optical properties. Clinical significance: The research emphasizes the promise of using cellulose nanocrystals (BCNCs) as an eco-friendly enhancer for zirconia-reinforced glass ionomer cement.