Until now, there has been a lack of analytical methods that can reliably verify the authenticity of organically grown plants and derived organic food products. In this study, stable isotope ratio analysis of hydrogen (H, δ²H), carbon (C, δ¹³C), nitrogen (N, δ¹⁵N), oxygen (O, δ¹⁸O) and sulfur (S, δ³⁴S) was conducted along the tomato passata production process using organic and conventionally grown tomatoes from two Italian regions over two years. A gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) based method was developed and applied for analysis of C and N isotope ratios in amino acids derived from tomatoes. Of the bulk isotope ratios, δ¹⁵N was the most significant parameter for discriminating organic from conventional products. The classification power was improved significantly by compound-specific isotope analysis regardless of the production years and regions. We conclude that isotope analysis of amino acids is a novel analytical tool for complementing existing certification and control procedures in the organic tomato sector.