This study investigated the feasibility of using natural fiber material to create honeycomb cores, as traditional cores made of aluminum, Nomex, and petroleum‐based materials are not environmentally friendly. The natural fiber honeycomb cores were formed using a 3D printed molding process and were bonded to flax and glass fiber facings to improve the durability of the structures. The addition of cellulose and nanoclay to the adhesive enhanced the flexural strength of the structures by 7.43% and 10.48%, respectively, while also absorbing 8.67% and 8.91% more impact energy than structures bonded with epoxy alone. However, the compressive strength decreased by 10.79% and 13.6% with the addition of cellulose and nanoclay to the adhesive, respectively. Tensile properties were also studied, and the tensile strength of hybrid facings was found to be 69.45% higher than those using solely flax facings. Additionally, hybrid facings effectively reduced moisture uptake, making them hydrophobic and reducing water uptake by 46.89% compared to solely flax facings. Overall, natural fiber honeycomb composite structures showed comparable performance to Nomex and aluminum honeycomb composites, offering favorable properties while being constructed using environmentally friendly materials. The efficient manufacturing process using additive manufacturing makes these structures readily customizable and scalable, leading to their implementation in numerous applications such as aerospace, automotive, and marine industries.