This study investigates priority assignment rules (PARs) for transaction processing in automated warehouses featuring a shuttle-based storage and retrieval system (SBSRS). By incorporating real-time data tracking through agent-based modeling, the research explores the unique aspect of the SBSRS design, which involves flexible travel of robotic order picker shuttles be-tween tiers. The paper proposes PARs under agent-based modeling to enhance multi-objective performance metrics, including average flow time (AFT), maximum flow time (MFT), outlier transaction AFT, and standard deviations of flow times (SD) within the system. Experimental evaluations are conducted with various warehouse designs, comparing the results against commonly used static scheduling rules. The findings demonstrate that real-time tracking policies significantly improve system performance. Specifically, prioritizing the processing of outliers based on transaction waiting time enhances MFT, SD, and other performance metrics, while minimizing adverse effects on AFT. Certain rules exhibit notable improvements in MFT and SD, while others achieve the lowest AFT values among all experiments. This paper contributes to the existing literature by presenting a multi-objective performance improvement procedure and highlighting the advantages of real-time data track-ing-based scheduling policies in automated warehousing systems.