Collaborative robots, or cobots, offer a unique combination of productivity and flexibility that has led to significant growth in adoption over the past decade. Moreover, recently, there has been a shift towards a human-centered design of the workspace, known as one of the drivers of Industry 5.0, which prioritizes the well-being of operators. To achieve this, various human factors such as ergonomics, mental workload, personal skills, and capabilities need to be considered in the workspace design, and their impact on system productivity must be evaluated. The integration of a human and a cobot in the same workplace can affect the performance of the human operator, as the perception of the cobot can impact their work. This highlights the importance of taking human factors into account, as a lack of consideration in these aspects has contributed to the failure of many implementations. To link the objectives of productivity, flexibility, and human factors consideration, a dynamic real-time multi-objective task allocation strategy for collaborative assembly systems is developed. This approach considers the different characteristics of the resources and optimizes for two objectives, makespan, and energy expenditure of the operator. By using this approach, it is possible to modify the behavior of the cobot by reallocating tasks between the two resources based on the operator’s current needs. In other words, if the operator appears too stressed due to time constraints or their energy rate level is too high, some of their assigned tasks can be transferred to the cobot. This helps to maintain a balanced system while reducing the operator’s stress.