We report a new electrophoretic set-up and method for rapid specificity screening of an immobilised enzyme against a range of substrates present in a mixture. The penicillinase-catalysed reaction is carried out on-the-fly, following separation of putative substrates and preceding separation of the reaction products. The new active pixel sensor detector gives an option of using multiple detection windows on a single flow line and enables efficient on-line monitoring of this heterogeneous biocatalytic process with multiple putative substrates injected simultaneously.