Waste products destined for landfills with high calorific value are increasingly being explored for potential use in a variety of industries. One example is the potential use of these wastes in cement kilns to reduce greenhouse gas (GHG) emissions from cement production. This study develops a cradle-to-gate life cycle assessment (LCA) model to estimate the GHG emissions, criteria air contaminants (CAC), and the impact of biogenic carbon accounting methods in biomass-containing alternative fuels (AFs) on life cycle GHG emissions when replacing natural gas with AFs at a cement facility. The proposed AF mixture includes landfill wastes like construction and demolition waste, asphalt shingles, tire fluff, carpet, textiles, and plastics. While many LCAs assume the biogenic fraction's climate impact is carbon-neutral, its actual effects depend on a range of new methods being proposed to account for the climate impacts associated with biogenic carbon. The findings of this study demonstrate a reduction of approximately 7–13% in life cycle GHG emissions. The preliminary estimates suggest that the change to CACs will likely not be materially different from the current use of natural gas. It also emphasizes the importance of accounting for the biogenic fraction in biomass-based AFs, indicating a potential overall reduction of up to 7.2% in life cycle GHG emissions when the biogenic fraction is treated as carbon-neutral. While factoring in the benefits of shorter rotation and longer storage periods results in a 12.7% reduction in life cycle GHG emissions. The LCA model developed in this study holds the potential for broad application among cement facilities that are considering fossil to alternative fuels as part of their GHG emission reduction strategies.