The design of multi-purpose batch plants is a challenging task, because the number of degrees of freedom for optimization is high. Important optimization variables are the scheduling, operating conditions and the sizes of the equipment items. Since all factors interact, a simultaneous consideration would be beneficial in order to reduce capital and operating costs. In this article, this complex task is tackled for a new case study of a sequential plant for protein production. The case study contains comprehensive models of the unit operations to evaluate equipment dimensions, mass balances and operating times. Variable changeover times and semicontinuous unit operations are considered. For optimization, a MINLP model is used that consists of smaller NLP and MILP submodels in order to simplify modeling. Simulation runs for different product demands are performed and it is shown that good solutions can be found in an adequate time. (C) 2016 Elsevier Ltd. All rights reserved.