The use of waste‐based bio‐fillers in composite manufacturing has increased in recent years due to their sustainable and biodegradable characteristics. The current study fabricates jute/banana (JB) fiber‐reinforced epoxy composites incorporating waste‐derived eggshell (ES) bio‐filler and investigates the effect of ES bio‐filler on the mechanical, morphological, and water absorption properties of the composites. JB fibers (1:1) and varying ES filler contents (5, 10, 15, and 20 wt%) were used to manufacture the composites using the hand lay‐up technique. Their tensile, flexural, and impact properties, microstructure, chemical compositions, and water absorption are then examined. It is found that the composite composed of 15 wt% ES exhibits better tensile and flexural properties with a tensile modulus and strength of 4.42 GPa and 95.27 MPa, and a flexural modulus and strength of 3.96 GPa and 117.47 MPa, respectively, whereas the composite filled with 5 wt% ES shows a maximum impact strength of 46.83 kJ/m2 and drops with increasing bio‐fillers. Scanning electron microscopy reveals that composite failures occur due to jute and banana fiber fractures, filler–fiber‐matrix debonding, fiber pullout, and ES filler agglomeration. Moreover, water absorption reduces as the ES content rises, and the 20 wt% ES filler‐based composite shows a minimum water absorption of 7.67% after 240 h. This study provides some insights to promote the usage of ES bio‐filler in natural fiber composites to improve their mechanical and water absorption properties and their potential applications in the internal structures of automobiles, aircraft, and construction.