Reconfigurable manufacturing has been designed to dynamically adjust the hardware, software, and logistics to rapidly match the system capability and functionality to the changing markets. The recent emergent mass personalization and mass individualization demands the future reconfigurable manufacturing systems (RMSs) with greater flexibility and adaptability, primarily due to the substantial increase in product variety and demand uncertainty. In this study, we investigate a manufacturing environment comprising multiple reconfigurable production lines that are designed to simultaneously produce a diverse product mix. These lines share modular components, enabling dynamic reconfiguration of each line in real time to adapt both capacity and functionality. Leveraging recent advances in smart manufacturing, we propose a real-time, autonomous coordination framework for RMSs. This framework enables autonomous production lines to coordinate collaboratively, enhancing the system’s responsiveness and collective ability to meet fluctuating market requirements. Our approach encompasses detailed modeling to automate the operations of each line, including configuration design, capacity planning, reconfiguration action planning, processing time allocation, and configuration path optimization for each individual line. Furthermore, we incorporate real-time information sharing among the lines and introduce a mathematical framework to support the autonomous coordination of stochastic demand. This includes a bidding-based mechanism for distributing demand and exchanging machines or modules (i.e., groups of machines) among lines. The proposed method enables adaptive configuration of lines and machines in response to shared demand while operating under constraints related to the limited availability of configurable components.