The present study evaluates the effects of incorporating quercetin-loaded nanogel (NG) made from soy protein isolate (SPI) and Xanthan-gum, along with nanocrystalline cellulose (CNC), into a matrix of starch and hydroxypropyl methylcellulose (HPMC) using the casting method. Scanning electron microscopy (SEM) images illustrated the notable influence of CNC and NG on the surface morphology of the films. Notably, the Starch/HPMC/CNC10% (SHN10) composite film enriched with 7 wt.% NGs (SHN10NGs7) exhibited a remarkable improvement in tensile strength performance, increasing from 7.9 ± 0.52 to 14.2 ± 0.41 MPa, accompanied by a reduction in elongation at break from 56.9 ± 2.51 to 8.8 ± 0.31. Moreover, SHN10NG7 film demonstrated notable antioxidant and antibacterial efficiency due to the quercetin release. Remarkably, the films exhibited significant inhibitory effects on both Escherichia coli and Staphylococcus aureus. In summary, the resulting composite film, comprising an optimized blend of CNC and NG, exhibited enhanced mechanical properties, improved barrier characteristics, and notable antibacterial activity. The findings suggest that the novel active packaging in this study can be a promising candidate for utilization as an active food packaging material, presenting opportunities for innovative applications in the realm of high-quality functional packaging materials.