Three-dimensional (3D) printing technology allows foods to be shaped into unique and complex. Chocolate is frequently used in food printing due to its extrusion melting capacity and attractiveness. In this study, chocolates enriched with ω-3 were produced with 3D printing technology. Using electrospraying, ω-3 was encapsulated within sodium alginate (SA) microparticles, and 3D printed chocolates were coated with those microparticles. Then, the ω-3 blend and ω-3-SA coated chocolates were compared. Before printing, the rheological properties of chocolate were analysed. In addition to their characteristics, the printed chocolates were evaluated for total phenolic content (TPC) and antioxidant capacity, in vitro gastrointestinal digestion, and ω-3 release profile. Fourier transform infrared (FTIR) spectroscopy indicated that ω-3 was successfully incorporated into the SA particles. According to the mechanical testing, the chocolate structures coated with ω-3-SA exhibited higher compressive strength than structures mixed with ω-3. The results revealed that the incorporation of alginate into pure chocolate scaffolds through the coating process resulted in an increase in compressive strength. The TPC and antioxidant capacities of ω-3-SA microparticles (NP) coated and ω-3 mixed chocolate samples were also significantly increased compared to those of pure chocolate after in vitro digestion. ω-3-SA NP-coated chocolate appeared to have a lower quality release profile. The faster release of encapsulated ω-3 at a pH value of 7 may be attributed to the fact that sodium alginate particles dissolve faster in high pH environments. This study revealed that 3D printing technology could be actively leveraged to create food-based products with the necessary ingredients to meet consumer demand.