The presence of lipids and urea in elasmobranch tissues can affect carbon (δ13C) and nitrogen (δ15N) stable isotope values, introducing bias in food web interpretations. Information on how lipids and urea affect δ13C/δ15N is only available for < 5% of ~ 1150 described elasmobranch species and results are highly variable among existing studies. Here, we investigate the effects of lipid and urea extraction on δ13C, δ15N, and C:N ratios in muscle and blood plasma of two batoids (Pastinachus ater and Himantura australis) and examine the influence of lipid/urea extraction on isotopic niche size and overlap. Lipid extraction (LE) did not affect δ13C, δ15N, or C:N ratios, suggesting low lipid content. Urea extraction (UE), however, increased δ15N and C:N in muscle. The ~ 1‰ δ15N increase represents a shift of ~ 0.5 trophic levels relative to bulk samples, highlighting the importance of UE to accurately assess trophic positions. Although there was no effect of any treatment on niche size, the probability of P. ater occurring within the niche of H. australis increased following UE. Overall, results suggest that urea should be removed from muscle prior to analysis, but LE is not required. Given the interspecific variability in the effects of lipid/urea on elasmobranch δ13C/δ15N, more studies are needed to assess the effects of lipid and urea on a broader range of species to produce a generalized understanding. Where no species‐specific data are available, we recommend pilot samples are analyzed to determine if LE is needed prior to preparation of the overall sample set.