Process monitoring is a crucial task for bioprocess optimization and will play a decisive role in the digitization of future bio-based production systems. System failure prediction technologies must be an integral part of monitoring schemes; however, these technologies are underdeveloped as far as the bioenergy industry is concerned. The objective of PRODIGIO is to establish a base of knowledge for the development of system failure prediction technologies that increase the performance of microalgae production and anaerobic digestion systems and advance towards more favourable techno-economic, environmental and social performance to achieve more sustainable microalgae biogas. By combining perturbation experiments in bioreactor systems and cutting-edge methods for big data analysis, PRODIGIO will decode the triggers, identify early-warnings, define threshold values, and calculate warning times for critical state transitions in bioreactors. Taking into account processes inefficiencies, we estimate that, along with the implementation of prevention countermeasures, PRODIGIO technology could contribute to increasing resource and energy efficiencies >50% throughout the production chain, which would translate into OPEX savings and GHG emissions reduction. The technological solutions that will derive from the project, such as a catalog of early warning signals for the failure of microalgae production and conversion-to-biogas systems, will be pre-commercial in nature; however, a roadmap will be compiled and updated during the course of the project that will identify priority research lines for further development and future implementation of technology. The results of PRODIGIO will pave the way for moving the entire microalgae biogas production chain efficiently towards its theoretical maximum, enabling the development of a fully integrated and truly sustainable microalgae biogas production industry and contributing to strengthening the EU's leadership in renewable fuel technologies.