Collaboration between humans and robots has great promise in manufacturing systems. The utilization of cobots in a manufacturing system can improve both productivity and ergonomics. In this paper, we study the problem of how to allocate limited cobot/robots to manufacturing systems with multiple workstations so that an integrated performance measure, considering both productivity and ergonomics is optimized. Previous work on cobot/robot allocation in manufacturing systems focus on the decomposition of tasks for a single workstation into multiple work elements, and then split them between human and robots, rather than studying multi-machine systems. To bridge this gap, we consider the allocation of cobots/robots to a multi-stage manufacturing system. Specifically, we establish an integrated performance measure and formulate cobot/robot allocation into a constraint integer programming problem. With this formulation, we obtain the optimal allocation of one available cobot/robot in simulated production systems, based on the integrated performance measure of productivity and ergonomics. Furthermore, the allocation problems of production systems with multiple cobots/robots is considered and solved with a scalable algorithm. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —Collaborative robots and independent robots are increasingly applied to manufacturing production systems. However, how to optimally allocate both types of robots considering both productivity and ergonomics influence has not been well studied. In this article, we established a practical optimization method to allocate cobots/robots to different workstations and split the work between cobot and human in one workstation when there are multiple workstations and a limited number of available cobots/robots in the manufacturing systems. Based on various real-world scenarios, we inferred useful insights for the robot/cobot allocation problem. To deal with the computational load when the number of workstations is large, a scalable optimization algorithm is also adopted. The case study results demonstrated the effectiveness of the proposed approach.