Recent advances in using biological scaffolds for nanoparticle synthesis have proven to be useful for preparing various nanostructures with uniform shape and size. Proteins are significant scaffolds for generating various nanostructures partly because of the presence of many functional groups to recognize different chemistries. In this endeavor, cocosin protein, an 11S allergen, is prepared from coconut fruit and employed as a potential scaffold for synthesizing Mn3O4 materials. The interaction between protein and manganese ions is studied in detail through isothermal calorimetric titration. At increased scaffold availability, the Mn3O4 material adopts the exact hexamer structure of the cocosin protein. The electrochemical supercapacitive properties of the cocosin-Mn3O4 material are found to have a high specific capacitance of 751.3 F g-1 at 1 A g-1 with cyclic stability (92% of capacitance retention after 5000 CV cycles) in a three-electrode configuration. The Mn3O4//Mn3O4 symmetric supercapacitor device delivers a specific capacitance of 203.8 F g-1 at 1 A g-1 and an outstanding energy and power density of 91.7 W h kg-1 and 899.5 W kg-1, respectively. These results show that cocosin-Mn3O4 could be considered a suitable electrode for energy storage applications. Moreover, the cocosin protein to be utilized as a novel scaffold in protein-nanomaterial chemistry could be useful for protein-assisted inorganic nanostructure synthesis in the future.