Organic–inorganic hybrid materials with nanoscale morphologies gain significant attention as a potential candidate for energy storage applications. Herein, nickel hydroxide (Ni(OH)2) and benzo[2,1,3]selenadiazole (BSe)‐capped dipeptide amphiphiles are electrodeposited over flexible nickel foam (NF) substrates to fabricate organic–inorganic nanohybrids. The in situ electrochemical deposition of organic–inorganic nanohybrids is investigated by Fourier transform infrared spectroscopy, X‐ray photoelectron spectroscopy, energy dispersive‐electron microscopy, and elemental mapping. The nanostructured morphology of the nanohybrid material is investigated by field‐emission scanning electron microscopy and transmission electron microscopy. The electrochemical performance and supercapacitor properties are examined in 1 m KOH aqueous solution. Aromatic diphenylalanine (FF)‐based nanohybrid BSeFF/Ni(OH)2 deposited on the NF electrode exhibit a specific capacitance of 1250 F g−1, whereas dileucine (LL)‐based nanohybrids BSeLL/Ni(OH)2 show a specific capacitance of 689 F g−1 at a current density of 2 A g−1.