Plants sustainably produce low levels of secondary metabolites of high industrial value. However, they are often too complex to be economically manufactured by chemical synthesis. Advanced metabolic engineering and exploitation of plants as Green Factories has been prevented due to poorly understood metabolic pathways in plants and the regulation thereof. SmartCell brings together 14 leading European academic laboratories and four industrial partners in order to create a novel concept for rationally engineering plants towards improved economical production of high-value compounds for non-food industrial use. Although SmartCell focuses on terpenoids, the largest class of secondary metabolites, which exhibit extremely diverse biological and pharmaceutical activities, all knowledge, tools and resources developed in the project, are generic and broadly applicable to engineer any plant biosynthetic pathway. A systems biology approach using metabolomics and transcriptomics is taken to move beyond the state of the art. New multigene transfer technologies are developed. By screening and functionally categorizing genes at structural, regulatory and transport levels a comprehensive knowledge base of how secondary metabolite biosynthetic pathways operate in plants is developed. The case study component i.e. manufacturing a valuable terpenoid in an optimized large-scale system gives SmartCell a unique opportunity to directly make transition from fundamental science to application. For long-term exploitation an integrated database, compound library, cell culture collection and a genebank available for academic and industrial communities will be established. SmartCell provides new opportunities for SMEs and established European biotech companies, and the technology can also be transferred to other e.g. fine chemical and pharmaceutical industries. SmartCell will prove that plant-based resources can furnish the European society and industry far more than they presently do.