The synergistic effect of nuclear (Sn) and electronic (Se) energy loss observed in some ABO3 perovskites has attracted considerable attention due to the real possibility to modify various near-surface properties, such as the electronic and optical properties, by patterning ion tracks in the defective near-surface regions. In this study, we show that low-energy ion-induced disordering in conjunction with ionizing ion irradiation (18 MeV Si, 21 MeV Ni and 91.6 MeV Xe) is a promising approach for tailoring ion tracks in the near-surface of defective KTaO3. Experimental characterization and computer simulations reveal that the size of these latent ion tracks increases with Se and level of pre-existing damage. These results further reveal that the threshold Se value (Seth) for track creation increases with decreasing pre-damage level. The values of Seth increase from 5.02 keV nm−1, for a pre-existing fractional disorder of 0.53 in KTaO3, to 10.81 keV nm−1 for pristine KTaO3. Above these thresholds, amorphous latent tracks are produced due local melting and rapid quenching. Below a disorder fraction of 0.08 and Se ⩽ 6.68 keV nm−1, the synergistic effect is not active, and damage accumulation is suppressed due to a competing ionization-induced damage annealing process. These results indicate that, depending on Se and the amount of pre-existing damage, highly ionizing ions can either enhance or suppress damage accumulation in KTaO3, thus providing a pathway to tailoring defects states. Comprehending the conflicting roles of highly ionizing ions in defective ABO3 oxides is vital for understanding and predictive modeling of ion-solid interactions in complex oxides, as well as for achieving control over ion track size in the near-surface of defective KTaO3.