Cement manufacturing is an energy-intensive and heavy pollutant emissions process. Waste-derived alternative fuels are widely used to reduce the pollutant emissions and the use of fossil fuel. Within the cement kiln, it requires about 40-50% of total thermal energy to complete the complex chemical reactions of clinker formation. High kiln temperature and the intrinsic ability for clinker to absorb and lock contaminants into the clinker allow the kiln to burn a wide range of alternative fuels. Agricultural biomasses are one of the emerging alternative fuels in the cement industry due to their availability and very low price. This chapter presents the effects of using agricultural biomasses as alternative fuels on the energy efficiency and emission from the kiln by using Aspen Plus process modeling. The suggested model is verified against measured data from industry and data available in literature. Results show that up to 3% of energy efficiency improvement along with 3.5% reduction of CO2 can be achieved through the utilization of various agricultural biomasses.