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In this study, we tackle a key scheduling problem in a robotic arm-based food processing system, where multiple conveyors—an infeed conveyor that feeds food items to robotic arms and two tray lane conveyors, on which trays to batch food items are placed—are implemented. The target scheduling problem is to determine what item on an infeed conveyor belt is picked up by which robotic arm at what position, and on which tray the picked up item will be placed. This problem involves critical constraints, such as sequence-dependent processing time and dynamic item and tray positions. Moreover, due to the speed of the infeed conveyor and latency in the information about entering items into the system, this scheduling problem must be solved in near real time. To address these challenges, we propose a scheduling solution that first decomposes the original scheduling problem into sub-problems, where a sub-problem formulated as a goal program schedules robotic arms only for a single tray. The performance of the proposed solution approach is then tested under a simulation environment, and from the experiments, the proposed approach produces acceptable performance.