Rationale: Concerns exist over observed shifts in value and variance of nitrogen isotopes following physicochemical extraction of lipids from organic matter. The mechanisms behind these apparent changes in bulk tissue delta N-15 values are not fully understood yet have major implications for analytical costs and integrity of data interpretations. Methods: Changes in proximate analysis, amino acid composition, C:N ratios, bulk tissue and amino acid delta C-13 and delta N-15 values, and resulting isotope-based food web metrics were compared between lipid-intact and lipid-extracted muscle tissue of fishes spanning <1% to >20% muscle fat content to identify mechanisms of nitrogen isotope fractionation associated with physicochemical lipid extraction. Results: Bulk delta C-13 and delta N-15 values increased and %N, C:N ratios and crude protein content decreased following lipid extraction. Resulting bulk isotope niche spacing and overlap varied significantly between lipid-intact and lipid-extracted tissues. While amino acid composition significantly changed during lipid extraction, particularly for lipid-associated amino acids (e.g., Glu, Lys, Ser), individual amino acid delta C-13 and delta N-15 values, and their associated compound-specific isotope analysis of amino acids (CSIA-AA)-based food web metrics, did not. Conclusions: Physicochemical lipid extraction caused significant tissue composition changes (e.g., leaching of amino acids and N-15-deplete nitrogenous waste) that affected delta C-13 and delta N-15 values and tissue %C and %N beyond simply removing lipids. However, lipid extraction did not alter individual amino acid delta C-13 or delta N-15 values or their associated CSIA-AA-based food web metrics.