Accurate analytical methods are required to develop and evaluate the quality of new renewable transportation fuels and intermediate organic liquid products (OLPs). Unfortunately, existing methods developed for the detailed characterization of petroleum products, are not accurate for many of the OLPs generated from non-petroleum feedstocks. In this study, a method was developed and applied to the detailed characterization of complex OLPs formed during triacylglyceride (TG) pyrolysis which is the basis for generating one class of emerging biofuels. This method uses gas chromatography coupled simultaneously with flame ionization and mass spectrometry detectors (GC–FID/MS). The FID provided accurate quantification of carbonaceous species while MS enabled identification of unknown compounds. A programed temperature vaporizer using a 25 °C, 0.1 min, 720 °C min −1, 350 °C, 5 min temperature program is employed which minimizes compound discrimination better than the more commonly utilized split/splitless injector, as verified with injections at 250 and 350 °C. Two standard mixtures featuring over 150 components are used for accurate identification and a designed calibration standard accounts for compound discrimination at the injector and differing FID responses of various classes of compounds. This new method was used to identify and quantify over 250 species in OLPs generated from canola oil, soybean oil, and canola methyl ester (CME). In addition to hydrocarbons, the method was used to quantify polar (upon derivatization) and unidentified species, plus the unresolved complex mixture that has not typically been determined in previous studies. Repeatability of the analytical method was below 5% RSD for all individual components. Using this method, the mass balance was closed for samples derived from canola and soybean oil but only ca. 77 wt% of the OLP generated from CME could be characterized. The ability to close the mass balance depended on sample origin, demonstrating the need for an accurate quantification method for biofuels at various stages of production.