High performance piezoelectric devices based on arrays of PVDF-TrFE nanofibers have been introduced in the literature for a variety of applications including energy harvesting and sensing. In this Research Article, we utilize uniaxial tensile test on arrays of nanofibers, microtensile, and nanoindentation and piezo-response force microscopy (PFM) on individual nanofibers, as wells as DSC, XRD, and FTIR spectroscopy to investigate the effect of annealing on microstructure, mechanical, and piezoelectric properties of arrays and individual electrospun nanofibers. For PVDF-TrFE nanofibers annealing in a temperature between the Curie and melting temperature (in paraelectric phase) results in similar to 70% increase in crystallinity of the nanofibers. The findings of our multiscale experiments reveal that this improvement in crystallinity results in similar to 3-fold increase in elastic modulus, and similar to 55% improvement in piezoelectric constant. Meanwhile, the ductility and tensile toughness of the nanofibers drop by similar to 1 order of magnitude. In addition, nanoscale cracks were observed on the surface of the annealed nanofibers; however, they did not result in significant change in the strength of the nanofibers. The results of this work may have important implications for applications of PVDF-TrFE in energy harvesting, biomedical, and sensor areas.