Natural fiber composites are increasingly gaining popularity as a cost-effective and environmentally friendly alternative to synthetic fibers. Incorporating a variety of fibers enhances mechanical properties. The arrangement of fibers plays a crucial role in determining the mechanical characteristics of laminate composites. Therefore, the primary objective of this study is to investigate how the stacking order of jute (J) and banana (B) fibers affects the mechanical behaviour of composites made from phenolic resins. Four different fiber mat stacking sequences (J/B/B/J, B/J/J/B, J/B/J/B, and J/J/B/B) were used for developing the eco-fiber composites using the heat-press technique. Several mechanical parameters were assessed, including tensile strength, flexural strength, impact strength, and inter-laminar shear strength (ILSS). The experimental results indicated that the JBBJ composite exhibits superior tensile strength (46.65 MPa) and modulus (993 MPa) compared to the other composites due to the presence of high-strength jute fibers on the surface. Additionally, the flexural strength of the JBBJ composite (87.24 MPa) was found to be noteworthy. It was observed that the impact strength of jute fibers surpasses that of banana fibers. Consequently, the JBBJ composite demonstrates higher values for energy absorption (0.482 J) and impact strength (120 J m−1) compared to the other composites tested. Moreover, the JBBJ composite displays higher inter-laminar shear strength and hardness values compared to BJJB, JBJB, and JJBB by 30%, 35%, and 43%, respectively. Scanning electron microscope microphotographs reveal strong correlational fracture failure mechanisms, indicative of improved mechanical properties in the JBBJ composite. Based on the experimental results, it is evident that the JBBJ composite can be utilized in lightweight applications.