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Prokaryotic cells are pivotal in meeting the global demand for biopharmaceuticals. However, challenges such as the absence of advanced technology for real‐time monitoring, standardized testing methodologies, and quality risk assessment of microbial activity have led to increased production costs, delays, and shortages of biopharmaceutical products. A thorough understanding of how biomolecule production interacts with microbial population structure and function is vital for improving continuous manufacturing and process automation. In this review, we discuss the current microbiological techniques that meet good manufacturing practice requirements in industrial settings, explore the advantages of monitoring and measuring biomass growth efficiency and turnover rates beyond regulatory criteria for product release, and provide a critical assessment of the current state of knowledge on bioassays and engineering tools for biomolecule yield measurement and monitoring. Furthermore, we identify areas for future development, potential applications, and the need for interdisciplinary innovation to drive future research, including advancing bioassays for biopharmaceutical wastewater risk. [ABSTRACT FROM AUTHOR]