European perch undergoes several ontogenetic dietary shifts during its lifetime. The present study focused on the variability in otolith shape caused by ontogenetic dietary changes in this species. A total of 172 specimens (7.5 to 27.5 cm TL) were caught by local fishermen in Lake Ladik from April to November 2019. Shape indices (SIs) and elliptic Fourier coefficients (EFCs) were calculated for each otolith. To detect ontogenetic changes in otolith shape, SIs and EFCs were compared among the three defined size classes (I, II, and III). Size-related groups were distinguished by both SIs and EFCs. Otolith shape analysis was more effective than morphometric analysis in distinguishing ontogenetic groups. Simultaneous use of both methods improved the classification success of each method alone. This study demonstrated that otolith shape of European perch is influenced by ontogenetic changes in diet. However, sexual maturity of the fish is also responsible for these variations in otolith shape.