Policies such as a low carbon fuel standard (LCFS) have incentivized oil refineries to lower the carbon intensity of their operations and the fuels they produce. Although an increasing number of refineries are co-processing biogenic feedstocks, determining the renewable content and carbon intensities of the co-processed fuels (and potential credits earned through policies such as a LCFS) has proven to be challenging. Various methods that might be used to track the green molecules and determine the carbon intensities of co-processed fuels were compared. Although the use of carbon 14 and mass balance have predominated, each of these methods has some advantages and disadvantages. To try to benefit from the strengths of each method, a combined direct (C14) and indirect (modified mass balance) approach was shown to give representative values. However, the quality and frequency of the information collected needs to be assured, as it can improve the quality of data needed to determine the carbon intensity of the final fuels.