Bioactive food compounds, such as lutein, have numerous health-promoting activities. However, they have poor chemical stability and bioavailability, limiting their efficacy. Thus, in this study, both hydrophobic (lutein) and hydrophilic (anthocyanins) were simultaneously encapsulated into starch/zein gels using an innovative coaxial 3D food printing. Briefly, lutein-loaded zein gel was employed as the core layer, while starch gel was used as the outer layer in a coaxial extrusion 3D printing. A spiral-cube-shaped geometry was used to investigate the effects of layer height (0.4-1 mm), nozzle size (0.33-0.08 mm), printing temperature (55-95 °C), and ink concentrations (10-15%). The effects of different zein concentrations (20, 40, and 60%) and printing speeds (4, 8, 14, and 20 mm/s) were also investigated. The 3D-printed samples were characterized using scanning electron microscopy, Fourier transform infrared spectroscopy, x-ray diffraction, microCT, chemical stability, and simulated digestion methods. The sample printed with a zein concentration of 40% at a printing speed of 14 mm/s exhibited the best shape integrity. When lutein was encapsulated in starch/zein gels, only 39% of lutein degraded after 21 days at 25 °C, whereas 78% degraded at the same time when crude lutein was studied. After storing at 50 °C for 21 days, 20% and 1% of lutein were retained in the lutein-loaded 3D print and control sample, respectively. With the developed 3D printing encapsulation approach, the bioaccessibility of lutein was increased by ~7-fold compared to the crude lutein. Similarly, anthocyanins’ chemical stability (42% vs. 70% degradation) and bioaccessibility (38% vs. 20%) were improved compared to the unencapsulated form, respectively. As a result, the developed dual-layered starch/zein encapsulation approach can serve as a platform technology to enhance the stability and bioaccessibility of both hydrophilic and hydrophobic bioactive compounds. The proposed approach allows the food industry to design functional foods loaded with bioactive compounds with higher flexibility and precision.