Conventionally, software tools for the design of bioprocesses have provided only limited business-related information for decision-making. There is an industrial need to investigate manufacturing options and to gauge the impact of various decisions from economic as well as process perspectives. This paper describes the development and use of a tool to provide an assessment of whole flowsheets by capturing both process and business aspects. The tool is demonstrated by considering the issues concerned when making decisions between two potential flowsheets for a common product. A case study approach is used to compare the process and business benefits of a conventional process route employing packed chromatography beds and an alternative that uses expanded bed adsorption (EBA). The tool allows direct evaluation of the benefits of capital cost reduction and increased yield offered by EBA against penalties of using potentially more expensive EBA matrix with lower lifetimes. Furthermore, the tool provides the ability to gauge the process robustness of each flowsheet option.