The past years have revealed increased participation of individual companies in Lean Manufacturing (LM) tools and principles across different industries around the world. Grain milling industry, being one of Botswana’s greatest source of food, is not excluded from developing constructive processes to improve the productivity of grain value chain. Shifting this industry from traditional production setups to meet the lean manufacturing principles is a catalyst for the country to be self-sufficient in grain products. This work present a case study of a wheat milling company and applications of some lean manufacturing tools to enhance performance in the grain milling industry. The discussion is based on the results obtained from the implementation of Lean Manufacturing tools in the production system of the case study company. Significant achievements have been observed in the company’s supply chain, with a clear view of continuous process improvement art, improved product and service quality and flexibility in the production process.