In this work, pectin-based active films with a cocoa bean shell extract, obtained after waste valorisation of residues coming from the chocolate production process, and zinc oxide/zinc nanoparticles (ZnO/Zn-NPs) at different concentrations, were obtained by casting. The effect of the active additive incorporation on the thermal, barrier, structural, morphological and optical properties was investigated. Moreover, the photocatalytic properties of the obtained films based on the decomposition of methylene blue (MB) in aqueous solution at room temperature were also studied. A significant increase in thermal and oxidative stability was obtained with the incorporation of 3 wt% of ZnO/Zn-NPs compared to the control film. The addition of 5 wt% cocoa bean shell extract to pectin significantly affected the oxygen barrier properties due to a plasticizing effect. In contrast, the addition of ZnO/Zn-NPs at 1 wt% to pectin caused a decrease in oxygen transmission rate per film thickness (OTR.e) values of approximately 50% compared to the control film, resulting in an enhanced protection against oxidation for food preservation. The optical properties were highly influenced by the incorporation of the natural extract but this effect was mitigated when nanoparticles were also incorporated into pectin-based films. The addition of the extract and nanoparticles resulted in a clear improvement (by 98%) in UV barrier properties, which could be important for packaged food sensitive to UV radiation. Finally, the photocatalytic activity of the developed films containing nanoparticles was demonstrated, showing photodegradation efficiency values of nearly 90% after 60 min at 3 wt% of ZnO/Zn-NPs loading. In conclusion, the obtained pectin-based bionanocomposites with cocoa bean shell waste extract and zinc oxide/zinc nanoparticles showed great potential to be used as active packaging for food preservation.