Cotton warehouses face unique inventory management challenges. This research addresses this challenge by proposing innovative strategies to enhance warehouse efficiency. Three key objectives are addressed: modeling cotton bale movements, evaluating an alternative to the current bale handling process, and evaluating an alternative to the current cotton bale marketing system. Results reveal significant cost savings. Changing bale receiving and placement strategy by using gin codes yields a $499,000 per-cycle reduction for an Oklahoma cotton warehouse case. Altering order fulfillment techniques, such as grouping 30 orders, saves $34,000 per cycle. Implementing quality-based bale substitution leads to a $1.3 million saving per cycle.