This study investigates aflatoxin contamination levels during the post-harvest processing of whole cottonseed into defatted cottonseed meal, a critical feed component in the dairy industry. Whole fuzzy cottonseed, a byproduct of cotton gins, undergoes various processes to extract oil and produce meal and hulls. These are either used as animal feed or soil amendments. However, aflatoxin contamination poses significant challenges due to strict FDA action levels for dairy and beef cattle feed. This contamination occurs when Aspergillus flavus infects crops under specific environmental conditions or through improper handling during post-harvest processes. Our research aims to document aflatoxin levels during each stage of post-harvest processing, from cleaning to meal formation. Preliminary findings suggest that certain stages may concentrate aflatoxins akin to other agricultural products like dried distillers’ grains and solubles (DDGS). The implications of these findings could be profound for the dairy industry, where low allowable aflatoxin levels impact both economic and animal health outcomes. The cottonseed post-harvest process consists of cleaning, delinting, hull removal, kernel flaking, oil extraction, and meal formation. Understanding how aflatoxin levels change during these steps is crucial for ensuring safe and high-quality defatted cottonseed meal for livestock consumption. Microbial levels increased by 4 orders of magnitude during the acid delinting process, from 7.0× 105 to 5.2 × 109 CFU/g, and 5 orders of magnitude during the mechanical delinting process, from 7.3× 105 to 1.5 × 1010 CFU/g for the inoculated cottonseed samples. Higher microbial load was associated with lower protein levels and lower fat acidity levels. Further research will shed light on the effects of aflatoxin concentration on the nutritional value of the final product.