Many commercial equine diets incorporate yeast-based probiotics, specifically Saccharomyces cerevisiae, for regulation of the hindgut microbiome and to enhance digestibility. However, there is a significant lack of mandatory standardization for label claims; while voluntary regulatory bodies exist, commercial products are not legally required to verify microbial presence or concentration. This study aims to accurately optimize DNA extraction, purification, and PCR protocols to verify the presence of specific probiotics in processed horse feeds. During molecular verification, there were often false-negative results due to the complex biochemical nature of the feeds and the low concentration of the probiotics in comparison with the feedstuffs. In order to combat this challenge, several commercially available feeds were analyzed comparing different polymerases and different DNA clean up kits for the best amplification and detection of the probiotic by endpoint PCR. This study highlights the technical challenges of detecting microbial DNA in processed feeds, as well as the importance of optimization for accuracy in molecular detection. This study also provides a pathway for quality control verification methods.