Abstract3D food printers facilitate novel customization of the physicochemical properties of food. This study aimed to investigate the impact of storage conditions on the inactivation of the human norovirus surrogate, Tulane virus (TuV), within 3D printed foods. TuV-inoculated protein cookie food ink (∽ 4 log PFU/g) was distributed into 18 3D food printer capsules (50 g each); half immediately underwent extrusion. Storage of the capsules and printed food products at 20 °C (0, 6, 12, and 24 h), 4 °C (0, 1, 3, and 5d), and − 18 °C (0, 1, 3, and 5d) was completed before analysis for TuV via plaque assays in addition to aerobic plate count, yeast and mold counts, and pH and water activity (aw) measurements. A significant 3-way interaction effect was observed between time, temperature, and storage method (capsule/print) (p = 0.006). Significant findings include: (1) A greater reduction in virions was observed in capsules after 24 h at 20 °C and (2) a substantial reduction in virions at 4 °C from day 0 to day 1 was observed, independent of storage method. Microbial indicators remained steady across temperatures, with storage temperature significantly impacting pH and aw. A significant two-way interaction effect (p = 0.006) was found between microorganism type (yeast/aerobic counts) and temperature. This research seeks to provide insights for the food industry and regulatory bodies in crafting guidelines for the safe storage and handling of 3D printed foods and inks.