There is an urgent need in low cost and fast technologies that enable the exploration of natural or induced biodiversity in plants. Biochemical phenotyping is often considered as particularly promising to identify given analytes that are linked to desirable plant phenotypes and that could be used as markers for plant performance. Over the past 15 years, metabolomics and other omics approaches have been intensively used to study plant phenotypes. Still, they do not enable routine screens of very large populations in breeding programs, probably because this would represent unaffordable financial investments for equipment and specialised engineers. Along the last century, biochemical phenotyping and -screening have nevertheless been successfully exploited in medicine, pharmaceutical research and agro-industry. In medicine, over 6000 biochemical procedures exploiting a large variety of concepts and equipment are available for routine diagnosis and therapeutic monitoring. Pharmaceutical companies have spent massive investments to screen for biologically active molecules, whereas in the agro-industry increasingly sophisticated biochemical analysis has been developed to control the quality of raw and transformed products. Microplate technology is a well-established technology, which originated from the medical field and benefited from huge investments by the pharmaceutical industry. It offers the possibility to operate a wide range of analyses at very low costs per sample in plant research. To illustrate the potential of microplate technology as a high-throughput phenotyping tool, a screen for tomato metabolic mutants is shown where 24 enzymatic traits have been measured in more than 1500 samples within only 1 month with a relatively small investment.