In this study, chemically modified walnut shells (WS) were used as the filling material for synthesis of bio‐based epoxy composites and added to the matrix at varied mass ratios (10%–50%). The shells were initially treated with alkali and then modified with three different organic acids (citric acid [CA], oxalic acid [OA], and formic acid [FA]). The WS were characterized by Fourier transform infrared spectroscopy, scanning electron microscopy (SEM)/energy‐dispersive X‐ray spectroscopy (EDX) and thermo gravimetric analyzer. The SEM and X‐ray diffraction were employed to observe the morphology of the composites. The influences of acid type and WS percentages on the mechanical, thermal and water sorption properties were investigated. The maximum tensile strength (124.8 MPa) was obtained with CA‐treated shells (CA‐WS) and followed by OA‐treated shells (OA‐WS) (117 MPa) and FA‐treated shells (FA‐WS) (96.5 MPa). Acid modification had a positive effect on Young's modulus as that of epoxy resins increased by 5.45%–50.91%. The treatment did not significantly affect hardness. The optimum amount of modified shells in the composites was found to be 20 wt%. Water sorption values changed in the range of 2.78%–3.42% for composites with 20 wt% WS and observed to increase with the filler amount in the composite. However, this trend and the slight decrease in thermal properties are not critical obstacles for the use of modified WS in the manufacture of inexpensive epoxy‐ and bio‐based eco‐friendly products.