Integrated optimal design problems for biochemical processes which consider simultaneously all aspects necessary for a rigourous design typically result in mathematical formulations which would almost certainly be intractable. We overcome this problem by decomposing the design problem into two stages. The first stage is a dynamic optimisation where equipment sizes, operating conditions, processing rates and times, etc. are determined assuming a finite intermediate storage policy and a fixed series of unit operations. The majority of the design parameters are then fixed for the second stage, which determines the optimum operating schedule and intermediate storage capacity for the plant. Further refinements to the equipment design may also be made. To enforce batch integrity and take advantage of a number of simplifications not present in most scheduling packages, a new scheduling formulation is developed for the second stage. This paper briefly describes the two stage design procedure, outlining the key features of both subproblems. An example problem is shown with a summary of the results.