Organ-on-a-Chip and Microfluidic Plant Cell Culture Systems: The Next Frontier for Controlled Secondary Metabolite Production and Real-Time Metabolomic Monitoring

Plant secondary metabolites remain indispensable for pharmaceuticals, nutraceuticals, and cosmeceuticals, yet conventional plant culture systems are increasingly limited by inconsistent yields, poor scalability, and inadequate capacity for real-time process monitoring. Microfluidic technologies and organ-on-a-chip (OoC) platforms, originally developed for mammalian biology, are now emerging as powerful tools to overcome these constraints. These systems enable laminar flow, precise gradient generation, single-cell resolution, and biosensor integration, providing unprecedented control over the cellular microenvironment and supporting non-destructive, real-time metabolomic monitoring. While recent reviews have surveyed plant microfluidics broadly covering developmental biology, single-cell phenotyping, and root–microbe interactions, this review provides, to our knowledge, the first synthesis focused specifically on organ-on-a-chip approaches for plant secondary metabolite biosynthesis and real-time metabolomic monitoring. Advances in device fabrication, including PDMS, paper-based, hydrogel, and thermoplastic materials, surface engineering, gradient-based elicitation strategies, and integration of optical, electrochemical, and mass spectrometric detection systems have also been critically examined. Special emphasis is placed on root-on-a-chip, shoot meristem, protoplast, callus, and 3D organoid platforms for studying cell wall mechanics, vacuolar dynamics, cytoskeletal responses, and signalling cascades. However, challenges remain in long-term culture stability and scalability; nonetheless, these technologies offer a roadmap toward programmable ‘plant biosynthetic factories’ to produce high-value natural products.