Bio-compatible and eco-friendly flexible piezoelectric nanogenerators with transparency are emerging energy devices for next-generation energy application. A novel high performance natural, biodegradable and flexible eggshell membrane – polyvinylidene difluoride (PVDF) based piezoelectric nanogenerator has been developed using a low-temperature solution and spin coating route. X-ray Diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR) and Raman patterns exhibited all characteristic signature peaks of the eggshell membrane and PVDF film. Piezoelectric pristine PVDF, eggshell membrane and eggshell membrane-PVDF layered structure based nanogenerators are fabricated using the flexible ITO coated PET substrate and spin coating technique. The fabricated device of eggshell membrane-PVDF layer exhibited better performance with very high output voltage and current of 15 V and 150 nA as compared to 2 V and 20 nA electric output generation from pristine PVDF film based device under same compressive strain, without electric poling. Dielectric properties of piezoelectric PVDF film and eggshell membrane-PVDF were also measured to analyze the working mechanism of the nanogenerator. Hybrid eggshell membrane-PVDF structure shows very high dielectric constant (260) as compared to pristine PVDF (22). A very high output voltage with an average value of 65 V was also obtained from electrical poled hybrid nanogenerator under force of about 10 kgf. Such high piezoelectric output voltage and current from biodegradable eggshell membrane-PVDF based flexible piezoelectric nanogenerator was attributed to dramatic increase in interfacial polarization, capacitance and improved piezoelectric properties of PVDF and triple helical structure created polarization induced electrical dipole moment in the eggshell membrane lattice. The results not only provide a new way to utilize the solid waste for generating green energy from mechanical vibration but also an agent to increase the performance of the PVDF based nanogenerator for powering next generation self-powered implantable medical devices with reduced e-waste elements.