Due to increasing product variety and uncertain demand for individualized products, companies need to constantly adapt their manufacturing systems to maintain an efficient production. Therefore, an increasing need for the consideration of flexibility in manufacturing system design can be observed. In this context, the concept of matrix-structured manufacturing systems (MMS) has attracted recent attention. MMS aim to achieve an efficient production by implementing a flexible material flow among stations and by deploying redundant resources for the operations, thus allowing flexible cycle times of stations and flexible material transport. This paper investigates the impact of material handling flexibility, equipment flexibility, and operation flexibility on the economic design of MMS. We conduct a numerical example to determine the impact of the flexibility types based on a mixed-integer linear program. The results demonstrate that the consideration of equipment flexibility and material handling flexibility during the design of MMS lead to economically beneficial configurations.