The service industry worldwide continues to face unprecedented challenges in decision-making and in managing the operations involved in delivering products at low cost and ever-faster delivery speeds. These pressures exert an even greater impact upon small- and medium-sized enterprises (SMEs) involved in this industry who, influenced by globalisation, have to respond by handling the dynamic complexity within their operational supply chain. Many larger firms have implemented Lean and Six Sigma (LSS) and end-to-end integrated real-time information systems (RTI) that provide the information and the mechanisms needed to support flexibility and prompt decision-making. The recent emergence of new technologies such as multi-agent systems (MAS) provides enhanced capability to address complexity and decision-making with greater ease of use at a reduced cost. Whilst the application of Lean and Six Sigma are supported by significant published research, the application of integrated LSS and MAS in food distribution, especially in SMEs, is not. This study seeks to provide research to address this shortcoming for SMEs within the food distribution sector within Saudi Arabia, how this integrated approach can offer considerable performance improvement in SMEs and provide a base for further contributions in this field. This research undertook an empirical case study in Saudi Arabia to test the application of LSS in a food distribution SME. This approach demonstrated a significant improvement in the Six Sigma for late delivery. A single-stage MAS application extended this improvement, demonstrating that there is value in its application. The study conducted a survey of 39 firms in this sector to gain an insight into their current practices and challenges. The findings indicated there was a lack of Lean and Six Sigma principles adopted and that a lack of use of interconnected real-time systems to support decision-making and complex operational SCs. These findings identified the opportunity to design a conceptual framework with a stepped approach that integrated LSS with MAS, which was then developed on a Java-Assisted DEvelopment Framework (JADE) platform and tested using real-world data in an SME empirical case study. The results of the sequence of applications and the final simulations proved that this integrated Lean multi-agent system (LMAS) solution offered such substantial improvements in quality, time and costs that the SME considered that those factors justified making its implementation a priority.