In the context of Industry 4.0, the matrix production concept represents revolutionary solutions from a technological and logistics point of view. In a matrix production system, flexible, configurable production and assembly cells are arranged in a grid layout, and the in-plant supply is based on autonomous vehicles. Adaptable and flexible material handling solutions are required to perform the dynamically changing supply-demands of standardized and categorized manufacturing and assembly cells. Within the frame of this paper, the authors describe the in-plant supply process of matrix production and the optimization potential in these processes. After a systematic literature review, this paper introduces the structure of matrix production as a cyber-physical system focusing on logistics aspects. A mathematical model of this in-plant supply process is described including extended and real-time optimization from routing, assignment, and scheduling points of view. The optimization problem described in the model is an NP-hard problem. There are no known efficient analytical methods to find the best solution for this kind of problem; therefore, we use heuristics to find a suitable solution for the above-described problem. Next, a sequential black hole–floral pollination heuristic algorithm is described. The scenario analysis, which focuses on the clustering and routing aspects of supply demands in a matrix production system, validates the model and evaluates its performance to increase cost-efficiency and warrants environmental awareness of the in-plant supply in matrix production.