Proteases play a crucial role in biological functions such as tumor progression and tissue homeostasis. Recently, protease-activated prodrugs have gained attention for their potential to enhance selectivity in tumor-targeted therapies. In this study, we report the engineering of substrate sequences for matriptase, a protease overexpressed in tumors and previously explored for prodrug activation in vivo. A peptide library containing millions of potential substrates was displayed on Escherichia coli, and flow cytometric sorting was used to isolate improved substrates based on cleavage efficiency. Hits were ranked by flow cytometry, and the top substrates exhibited k(cat)/K(M) values over 40-fold higher than previously reported sequences. These substrates were further evaluated in an antibody-prodrug format, demonstrating exceptional activation. The matriptase substrates hold broad potential for applications such as cleavable linkers in next-generation antibody prodrugs. Furthermore, the developed bacterial display platform shows promise for discovering substrates of other proteases.