In view of current climate and energy policies, the cement industry is striving to save emissions and is increasingly using alternative fuels (AF) for the clinker burning process. AF are generally more coarse-grained and have a higher probability to fall incompletely burned onto the clinker bed, where they become embedded and can lead to changes in the material by locally causing reducing conditions. However, the qualitative and quantitative understanding of relationships between fuel particle sizes and the resulting material properties of the clinker is still limited. Here, we show experimentally that local reducing conditions can indeed lead to the reduction of iron and thus to local changes of the phase assemblage. The altered oxygen partial pressure within the pore volume of the sample also causes a brown coloration of the clinker. The extent of the changes was found to depend on the fuel particle size and the residence time of the embedded fuel particles in the clinker bed in the kiln. The new qualitative and quantitative data enable the optimization of the clinker burning process, which in turn can lead to an increasing use of AF in the future.