In this study, an active biofilm was developed by incorporating red dragon fruit peel (RDF) extract into soy protein isolate (SPI) film matrix for sustainable food packaging. The addition of betalain-rich-RDF extract (1–7 wt%) significantly improved UV-blocking and antioxidant properties of the film compared to the control film. As wt% of RDF-extract increased, water vapor permeability, water solubility, and elongation at break decreased by 1.06 × 10–10 g m m−2 s−1 Pa−1, 34.25%, and 133.25%, respectively. On the other hand, Tensile strength increased significantly (P < 0.05) by 78.76%. FTIR results confirmed the intermolecular interaction between RDF extract and SPI through hydrogen bonding, while XRD result showed a decrease in the crystallinity degree of the film with RDF extract addition. However, no significant change in the TGA curve between extract-incorporated SPI films was observed. SEM analysis revealed that SPI B and SPI D films had a more compact and denser structure than the control film, while AFM analysis showed an increase in Ra and Rq values representing higher surface roughness of SPI D film. SPI D film also significantly (P < 0.05) decreased the weight loss and increased total soluble solids of freshly cut apples over 7-day storage period.