This paper investigates the valorization of peanut shell powder (PSP), an abundant agro-industrial residue, as a biofiller for the development of sustainable 3D printable PLA-based composites for food packaging applications. A low-filled biocomposite containing 2.5 wt.% PSP was successfully processed into filament with dimensional tolerances suitable for fused deposition modeling printing. Thermal and melt flow analyses demonstrated that PSP marginally reduced the thermal stability of PLA while preserving its thermal transition temperatures and increasing the melt flow rate up to 51%. Differential scanning calorimetry revealed a slight increase in crystallinity in biocomposite filament compared to neat PLA pellets, mainly associated with thermo-mechanical processing of the extrusion, while the lower crystallinity degree relative to PLA extrudate suggested a negligible nucleating effect of PSP. To optimize print quality, different extrusion temperatures and infill flow rates were evaluated. The best mechanical performance was achieved at 200 °C and 130% flow rate, where reduced inter-filament porosity (5.2%) resulted in improved tensile strength and stiffness compared with the other printing conditions. Although mechanical properties remained lower than neat PLA, the material proved suitable for non-structural packaging applications. Prototype packaging boxes were fabricated and tested for the storage of fresh-cut melon. Compared with neat PLA packaging, the PLA-PSP system better preserved fruit firmness over 10 days, inhibited fungal growth, and delayed visible deterioration, highlighting the potential active role of PSP in food preservation. Anaerobic biodegradation tests conducted under mesophilic conditions confirmed that the addition of PSP did not hinder PLA biodegradability and slightly enhanced methane production. Overall, the results demonstrate that peanut shell waste can be effectively upcycled into functional 3D-printable biocomposites for sustainable packaging solutions.