Within the European project INCOVER, an experimental microalgae-based treatment system has been built for wastewater reuse and added-value products generation. This article describes this new experimental plant and the start-up stage, starting from the new design of three semi-closed horizontal photobioreactors with low energy requirements for microalgae cultivation (30 m3 total), using agricultural runoff and urban wastewater as feedstock. The inflow nutrients concentration is adjusted to select cyanobacteria, microalgae able to accumulate polyhydroxybutyrates, which can be used for bioplastics production. Part of the harvested biomass is used as substrate for anaerobic co-digestion (AcoD) with secondary sludge to obtain biogas. This biogas is then cleaned in an absorption column to reach methane concentration up to 99%. The digestate from the AcoD is further processed in sludge wetlands for stabilization and biofertilizer production. On the other hand, treated water undergoes ultrafiltration and disinfection through a solar-driven process, then it is pumped through absorption materials to recover nutrients, and eventually applied in an agricultural field to grow energy crops by means of a smart irrigation system. This plant presents a sustainable approach for wastewater management, which can be seen as a resource recovery process more than a waste treatment.