In this paper, we refer to a real case study of an industrial partner recently committed to its project on the design of a multi-unit and multi-product manufacturing system. Although the considered problem refers to an actual complex manufacturing system, it can be theoretically classified as a union of two key problems that need to be solved during the transfer line design stage: the transfer line balancing problem (TLBP) and the buffer allocation problem (BAP). As two closely related problems, TLBP and BAP usually have similar optimizing directions and share the same purpose: finding a balance between the performance of the transfer line system as well as minimizing investment costs. These problems are usually solved sequentially, but this leads to solutions close to a local optimum in the solution space and not to the global optimum of the overall problem. This paper presents a multi-objective optimization for concurrently solving transfer line balancing and buffer allocation problems. The new approach is based on a combination of evolutionary and heuristic-based algorithms and takes into account the uncertainty of market demand. To validate the proposed approach, an industrial case study in a multi-unit manufacturing system producing multiple products (four engine blocks) is discussed.