The problem of integrated design and control of bioprocess plants is considered. A previously presented optimization approach for biochemical systems based on linear programming and modeling using the power law formalism (the Indirect Optimization Method, IOM) is extended. This method is enhanced in order to take into account both static and dynamic measures, and its use for the optimization of the integrated design of a bioprocess is illustrated. The chosen case study is a wastewater treatment plant, a bioprocess which typically presents controllability problems in real practice due to bad design methodologies. After defining an objective function reflecting both investment costs and "paracosts" (such as stability, flexibility, and controllability), a set of constraints determined by the system components and technical and economical factors is defined. A comparison of the results obtained with this new method and with a global optimization method reveals that, in both cases, significant improvements in both controllability and cost reduction are achieved, although the global method yields somewhat better improvements. The advantages and limitations of both methods are evaluated, concluding that the IOM, through its incorporation to a dynamic process simulator, can be successfully used to obtain, in a quick, inexpensive and interactive way, near-optimal integrated designs for bioprocess plants.