The food and beverages (F&B) industry is believed to be the most thriving in the manufacturing sector in Nigeria, and as such is expected to contribute significantly to economic growth and national development, but analysis of available statistical data reveals myriads of operational inefficiency that have hindered optimum performance in the sector. The study examined how the implementation of Lean Manufacturing System (LMS) affects the operational efficiency of a leading company in the F&B industry (Nestle Nigeria Plc.). The study employed the usage of Data Envelopment Analysis to access the operational efficiency of the system. It was discovered that the average operational efficiency score improved to 98?ter the implementation of the lean system as against the 90% average performance before the implementation. It is also observed that the company attained a 100% optimal efficiency for five years (2010, 2012, 2013, 2014 and 2015) as against only one year (2001) in the period before the adoption of the lean system. The study discovered that a positive and a significant relationship exist between the Lean Manufacturing System (LMS) and the operational efficiency of the system as seen by the respective P-values of 0.11 and 0.026 before and after the implementation of the lean system. It was therefore recommended that the sampled company and others along the same value chain should seek to become a lean enterprise in order to improve their operational efficiency.