The use of biobased heterogeneous catalysts made from agricultural waste for producing biodiesel has gained attention for its potential to create a sustainable and low-cost process. The blending of two or more biomass residues to create more viable biobased catalysts is still in its early stages. In this study, a Biobased Composite Heterogeneous Catalyst (CHC) was made by blending the shells of periwinkle (PWS), melon seed-husk (MSH), and locust bean pod-husk (LBP) at a mixing ratio of 67:17:17 using Simplex Lattice Design Mixture, that was then calcined for 4 h at 800 °C. The chemical, structural, and morphological components of the CHC were characterized via XRF, XRD, SEM-EDX, BET, TGA/DSC, and FTIR to assess its catalytic potential. The CHC was employed to synthesize biodiesel from palm kernel oil, and the process optimization was conducted using the Taguchi approach. The XRF analysis showed that the catalyst had 69.049 of Calcium (Ca) and 9.472 of potassium (K) in their elemental and oxide states as 61.592% calcium oxide and 7.919% potassium oxide. This was also supported by the EDX result, that showed an appreciable value of 58.00% of Ca and 2.30% of magnesium, that perhaps provided the active site in the transesterification reaction to synthesize biodiesel. The morphological and physisorption isotherms via SEM and BET showed mesoporous structures in the CHC that were made up of nanoparticles. A high maximum biodiesel yield of 90.207 wt.% was attained under the optimized process conditions. The catalyst could be reused for up to four cycles, and the biodiesel produced met both ASTM D6751 and EN 14214 standards for biodiesel. This study demonstrates that blending PWS, MSH, and LBP waste materials can produce high-quality biodiesel without the need for additional catalysts.