In this work flexible composite nanogenerators were prepared aiming to identify and optimize the exploitation of the piezoelectric effect in mechanical energy harvesting. A novel shape-controlled synthesis of ZnO microstructures through hydrothermal route was achieved resulting in different morphologies and aspect-ratio particles, microwires, multipods, and desert-roses. The three different microparticles and round-shaped commercial nanoparticles were incorporated into a polydimethylsiloxane matrix and a comparative study on the piezoelectric output power dependence on the filler morphology was carried out. The highest performances, i.e. output voltage of 10V and a maximum power of 55µW, were obtained with the highest aspect-ratio ZnO filler, the microwires, dispersed in the PDMS matrix at a 40wt% concentration. Considering the generated voltage dependence on the size and aspect-ratio of the fillers, a working mechanism was formulated. The nanogenerators were then exploited to charge a homemade carbon-based supercapacitor. The voltage charging curves confirm the voltage generation trend based on the high aspect-ratio particles, showing that the best performances are obtained by the microwires-based composite nanogenerator. This work thus contributes to clarify the piezoelectric mechanism in composite nanogenerators and to maximize the output power generation in view of self-powered nanodevices able to recover and store waste environmental energy.