1. Stable isotopes represent a unique approach to provide insights into the ecology of organisms. δ13C and δ15N have specifically be used to obtain information on the trophic ecology and food web interactions. The trophic discrimination factor (TDF, Δ13C and Δ15N) describes the isotopic fractionation occurring from diet to consumer tissue and this value is critical to obtain precise estimates within any application of δ13C and δ15N. It is widely acknowledged that metabolism influences the TDF, being responsible for different TDFs between tissues of variable metabolic activity (e.g. liver vs. muscle tissue) or species body size (small vs. large). However, the connection between the variation of metabolism occurring within a single species during its ontogeny and TDFs has rarely been considered. 2. Here, we conducted a 9-month feeding experiment to report Δ13C and Δ15N of muscle and liver tissue for several weight classes of Eurasian perch (Perca fluviatilis), a widespread teleost often studied using stable isotopes, but without established TDFs for feeding on a natural diet. In addition, we assessed the relationship between the standard metabolic rate (SMR) and TDFs by measuring their oxygen consumption of the individuals. 3. Our results showed a significant negative relationship of SMR with Δ13C, but not with Δ15N of muscle or TDFs of liver tissue. SMR was significantly higher in perch juveniles, which translated to significantly lower Δ13C of muscle tissue. 4. In summary, our results emphasize the role of metabolism in shaping specific TDFs (i.e. Δ13C of muscle tissue), and especially highlight the substantial differences between individuals of different ontogenetic stages within a species. Our findings thus have direct implications for the use of stable isotope data and the applications of stable isotopes in food web studies.