The study of the piezoelectric response in praseodymium-doped (Na0.41K0.09Bi0.5)TiO3 (NKBT) revealed an unusual behaviour at doping level near 0.5 and 1.0 at%. Although there is a marginal increment in the piezoelectric charge coefficients for samples with praseodymium doping of 0.5–1.0 at% compared to undoped NKBT, importantly, the response drastically diminishes for doping concentrations exceeding 1.0 at%. To comprehend the observed anomaly, X-ray photoelectron spectroscopy (XPS) and temperature dependent conductivity measurement was carried out. These investigations provided critical insights into the role of oxygen vacancy and the behaviour of praseodymium ions in the NKBT matrix. The XPS analysis revealed the presence of core level peak corresponding to O-1s with asymmetric broadening at higher energy side implying the presence of oxygen bound to the perovskite lattice (binding energy: 529.2±0.3 eV) along with oxygen vacancy (binding energy: 531.5±0.4 eV). The XPS study further revealed that the concentration of the oxygen vacancy is lowest around 0.5 at% of praseodymium doping and beyond this the oxygen vacancy increases. The high temperature conductivity measurement supported these findings by showing similar trends in the electrical conductivity. Both the XPS and conductivity measurements further corroborate the conjecture that praseodymium behaves as amphoteric ion. The praseodymium occupies the A-site of perovskite (Na0.41K0.09Bi0.5)TiO3 for lower praseodymium concentration (<1.0 at%), whereas for higher doping concentration (>1.0 at%) it occupies the B-site exhibiting acceptor like behavior that deteriorates the piezoelectric response.