The present invention relates to a computer implemented method (600) for optimization of a bioprocessing system (100) formed by interconnected or interconnectable bioprocessing units and configured to provide a desired system functionality, the method comprising obtaining (610) requirement data of a bioprocess, the requirement data being at least indicative of the desired system functionality, and indicative of a desired substance resulting from the operation of the bioprocess system, obtaining (620) unit data indicative of characteristics of a plurality of bioprocessing units, generating (630) at least one optimized or suitable bioprocessing system configuration capable to provide the desired system functionality, the bioprocessing system configuration comprising a selection of bioprocessing units from the plurality of bioprocessing units selected using the requirement data, the unit data and an objective function dependent on the requirement data and the unit data. The invention extends to a configuration system (500).