A rapid method for designing integrated bioprocesses, using a combination of a windows of operation and a Pareto optimisation approach, is described in this paper. Within bioprocesses, multiple objectives are common, and achieving a satisfactory trade-off amongst the design objectives is crucial. Conventional optimisation results in the identification of the best operating policy for a given desired performance but gives little insight into how the process performance changes in the vicinity of the solution. In this paper, we explore the use of a Pareto optimisation technique to locate the optimal conditions for an integrated bioprocessing sequence and the benefits of first reducing the feasible space by the development of a series of windows of operation to provide a smaller search area for the optimisation. The final results are then presented in performance trade-off graphs and look-up tables, which give the design engineer an easily manageable solution set to work with. In this way, the decision-making procedure for design is made faster and more transparent. Two case studies illustrate the results from this integrated design methodology, some of which are counter-intuitive compared with the general design experience.