Low-carbon fuels, feedstocks, and energy sources can play a vital role in the decarbonization of clinker production in cement manufacturing. Fuel switching with renewable natural gas, green hydrogen, and biomass can provide a low-carbon energy source for the high-temperature process heat during the pyroprocessing steps of clinker production. However, up to 60% of CO2 emissions from clinker production are attributable to process-related CO2 emissions, which will need the simultaneous implementation of other decarbonization technologies, such as carbon capture. To evaluate the potential of fuel switching and carbon capture technologies in decarbonizing the cement industry, a study of the facility-level CO2 emissions is necessary. This study evaluates the potential for using a single low-carbon fuel as an energy source in clinker production for cement manufacturing compared to conventional clinker production (which uses a range of fuel mixes). In addition, conventional carbon capture (operated with natural gas-based steam for solvent regeneration) and electrified carbon capture configurations were designed and assessed for net-zero emission targets. Carbon emissions reductions with and without biogenic emissions credits were analyzed to ascertain their impact on the overall carbon accounting. Results show that carbon emissions intensity of cement can vary from 571 to 784 kgCO2eq/metric ton of cement without carbon capture and from 166.33 to 438.66 kgCO2eq/metric ton of cement with carbon capture. We find that when biogenic carbon credits are considered, cement production with a sustainably grown biomass as fuel source coupled with conventional carbon capture can lead to a net-negative emission cement (−271 kgCO2eq/metric ton of cement), outperforming an electrified capture design (35 kgCO2eq/metric ton of cement). The carbon accounting for the Scope 1, 2, and biogenic emissions conducted in this study is aimed at helping researchers and industry partners in the cement and concrete sector make an informed decision on the choice of fuel and decarbonization strategy to adopt.