Assembly systems require to be designed considering flexibility from a holistic perspective to produce the variety of current and future product generations. Reactive ad hoc changes after realizing both the product and assembly system designs require considerable effort and may even be impossible. A systematic collaborative approach that concurrently considers the early phases of product and assembly system development appears to be essential for working with long-term changes. To this end, a greater understanding of the working procedures and design activities concerning flexibility is required. In this paper, this is investigated based on a theoretical framework and a multiple case study at a world-leading manufacturer of heavy-duty vehicles. As a result, a developed early phase design process to enable long-term flexibility in assembly systems is presented. The theoretical implications provided and the findings are also relevant to those involved in the design process of flexible assembly systems.