The article evaluates the reduction of carbon dioxide emission due to the partial substitution of coal with alternative fuels in clinker manufacture. For this purpose, the calculations were performed for seventy waste-derived samples of alternative fuels with variable calorific value and variable share in the fuel mixture. Based on annual clinker production data of the Polish Cement Association and the laboratory analysis of fuels, it was estimated that the direct net CO2 emissions from fossil fuel combustion alone were 543 Mg of CO2 per hour. By contrast with the full substitution of coal with alternative fuels (including 30% of biomass), the emission ranged from 302 up to 438 Mg of CO2 per hour, depending on fuel properties. A reduction of 70% in the share of fossil fuels resulted in about a 23% decrease in net emissions. It was proved that the increased use of alternative fuels as an additive to the fuel mix is also of economic importance. It was determined that thanks to the combustion of 70% of alternative fuels of calorific value from 15 to 26 MJ/kg, the hourly financial profit gain due to avoided CO2 emission and saved 136 megatons of coal totaled an average of 9718 euros. The results confirmed that the co-incineration of waste in cement kilns can be an effective, long-term way to mitigate carbon emissions and to lower clinker production costs. This paper may constitute a starting point for future research activities and specific case studies in terms of reducing CO2 emissions.