Enhanced piezoelectric and energy-harvesting characteristics of Mn-doped (Na0.5K0.5)NbO3 (NKN) nanofibers have been investigated with actual fabrication of potential flexible nanogenerators. The electrospinning process of nanofibers has been initially optimized with the proper level of chelating agent and annealing temperature. High quality nanofibers are successfully obtained only by means of a certain level of doped-Mn, which incorporates into the NKN perovskite structure and facilitates significant grain growth. A single-particle-stacked structure along the direction of fiber length becomes more evident with increasing Mn content. An XPS analysis confirms that Mn exists in multivalent states of Mn2+/Mn3+. The effective piezoelectric coefficient of the nanofibers is found to be enhanced by 5 times with Mn-doping up to 3 mol % as characterized by piezoelectric force microscopy. The resultant flexible nanogenerators on PES films have exhibited similar to 0.3 V output voltage and similar to 50 nA output current under a bending strain.