Cement manufacturing is an energy intensive and heavy pollutant emissions process with energy typically accounting for 50% - 60% of the production costs. It is accountable for CO2, NOX, SO2 emissions and some heavy metal discharge from the pre-calciner kiln system which causes severe greenhouse effects. Energy efficiency improvement and how to reduce greenhouse gas emissions are thus most important areas of research. This paper focuses on reducing pollutants emissions by optimizing the usage of alternative fuels. A process model of the preheater tower calciner has been developed using Aspen Plus simulation software in this study based on the combustion mechanism. The model is verified against measured data from industry and data available in the literature. This paper presents the effects of the flow rate of alternative fuels and tertiary air on the composition of the flue gas in the preheater calciner. The effects of the fuel combustion on the NOx, and CO2 concentrations in the flue gas are also investigated. Three different alternative fuels, namely waste tyre, spent pot liner and municipal solid waste are considered for the study. Substitution rate of conventional fuel by the alternative one is also taken in consideration to identify its effect on the pollutant emission. Simulation results presented in this paper are considered useful to the cement manufacturing stakeholders to choose the right alternative fuel.