Nickel pyrophosphate nanostructures have been synthesized by a simple co-precipitation method. Annealing temperature affected the crystal structure formation of α-Ni2P2O7 and altered the surface morphology. By increasing the annealing temperature from 350 °C to 900 °C, the morphology of the material varies from irregularly shaped agglomerated particles to dumbbell-shaped nanoparticles respectively. The electrochemical performance of α-Ni2P2O7 nanoflakes (NP-2) and dumbbell-shaped (NP-3) nanoparticles is tested at 1 M KOH electrolyte solution, which provides the maximum specific capacitance of 146 and 121 F g−1 at a current density of 0.8 A g−1 respectively. Furthermore, the antibacterial activity of NP-2 nanoflakes is tested against different pathogenic Gram-positive and Gram-negative bacteria. The highest value of the inhibition zone exhibits the good antibiotic nature of the α-Ni2P2O7 nanoflakes.