Drum–Buffer–Rope is a theory of constraints production planning methodology that operates by developing a schedule for the system’s first bottleneck. The first bottleneck is the bottleneck with the highest utilization. In the theory of constraints, any job that is not processed at the first bottleneck is referred to as a FREE good. FREE GOODS do not use capacity at the first bottleneck, so very little attention is given to them in the Drum–Buffer–Rope literature. The objective of this paper is to present a methodology that improves the Drum–Buffer–Rope material flow management with attention to the second bottleneck and FREE GOODS. This paper presents a comparative analysis of Drum–Buffer–Rope material flow management and the proposed methodology in a job shop environment. To study the impact of FREE GOODS and the second bottleneck on the performance of the DBR method, 18 job shop simulation models were developed and data analysis was done for each simulation model. Lead time and throughput are the system performance measurement output parameters. The simulation result shows that the proposed methodology significantly improved the lead time and throughput.