The Swiss microalgae sector is still incipient and fragmented despite the massive increase in the demand for algae-based products in Europe. Although microalgae can improve sustainability in several agro-industrial sectors, some gaps in microalgal production technology still need to be overcome. For example, the optimal downstream processes remain unclear. Optimalgae aims to optimize downstream operations of microalgae production (i.e., harvesting, media recycling, and biomass processing and storage) according to its application. This approach is critical for implementing a biorefinery framework that increases the sustainability and circularity of microalgae production systems. Application-based optimized harvesting, post-treatment, and conditioning of microalgae reduces the ecological footprint and enhances efficiency and productivity. Optimalgae aims to be the next step in microalgae biotechnology by developing case-specific, application-oriented systems. This will culminate on the state-of-the-art 50m3 system (the biggest in Switzerland) at the new Agroscope site in Posieux, and the 1m3 mobile plant as a proof-of-concept of the onfarm decentralized biomass production.