The life-cycle greenhouse gas (GHG) emissions of alternative fuels that are capable of replacing conventional, petroleum-derived gasoline and diesel continue to be scrutinized for policy implementation. These alternative fuel technologies can also produce a number of value-adding nonfuel coproducts that require thorough and rigorous assessment in order to achieve an accurate life-cycle GHG emissions value. By using the gas to liquids (GTL) diesel pathway as a proxy for other alternative fuel pathways with coproducts, this paper examines how integration of coproduct analysis using the substitution method is possible within the existing framework and functionality of the GREET model. Using this approach, a GREET-compatible external tool was developed to calculate the life-cycle inventory of GTL coproducts to determine the life-cycle GHG emissions of GTL diesel using the substitution method. In addition to having built-in regional scenarios, this tool allows the user the flexibility to configure a given GTL product slate and to calculate the life-cycle GHG emissions of GTL diesel based on a given product composition. Using this protocol, the life-cycle GHG emissions of GTL diesel can range from 71.7 to 95.7 gCO2e/MJ on a well to wheel basis, with the range in carbon intensity being dependent on the mix of coproducts. These results highlight a weakly understood relationship between fuel and chemical products in LCA models. The coproduct integration approach described herein could potentially be incorporated into fuel LCA models, such as GREET, to allow users to further understand the potential environmental benefits of alternative fuel pathways, such as GTL.