The deliberate control of complex microbiomes is notoriously difficult and current approaches are often guided by simple trial-and-error. Advances in quantitative analysis modelling and design of these systems are urgently needed to improve the predictability and enable exploitation of the amazing synthesis capacities of microbiomes. The PROMICON project will learn from nature how microbiomes function through development and application of quantitative physiology, imaging, cell sorting machine learning and systems biology. This will be used to steer existing microbiomes towards production and to generate new synthetic microbiomes inspired by nature through an iterative design-build-test-learn cycle. The new consortia will also contain strains developed through systems metabolic engineering and will be used for the production of energy carriers, drop-in chemical feedstocks and advanced biomaterials. PROMICON will advance characterization tools to understand which strains (modules) are needed for a successful microbiome. It will identify the primary producers (farmers), secondary converters (labourers) and essential strains for microbiome stability (balancers). This knowledge will be used to reduce complexity of natural microbiomes for optimized production of phycobilli protein based pigments, exo-polysaccharides (EPS) and poly-hydroxyalkanoates (PHA) in a top-down approach. Secondly, synthetic microbiomes with increasing complexity (bottom-up) will be assembled for the production of butanol, H2 and PHACOS, a functionalized antimicrobial polyester. PROMICON will develop new reactor concepts and downstream processing for microbiomes and conduct early-stage life cycle assessment (LCA) to prepare exploitation. This ground-breaking project will not only inspire completely new production pathways and a paradigm shift from monocultures to mixed cultures in biotechnology, but also has the potential beyond biotechnology to inspire novel treatment options in biomedicine.