Due to increasing product variety and uncertain demand for highly individualized products, a rising need for flexibility of manufacturing systems can be observed. In this context, the concept of matrix-structured manufacturing systems (MMS) has attracted increasing consideration. MMS aim to achieve high operational flexibility by implementing a flexible product flow between stations with automated guided vehicles and by providing redundant resources for each operation, thus eliminating constant cycle times and the serial arrangement of stations. This paper investigates the design of MMS pursuing an economic objective. We formulate a mixed-integer program for the design of MMS. Introducing a numerical example, we illustrate the effectiveness of our approach and derive future research opportunities.