This study evaluates the comprehensive valorization of the byproducts derived from the two-phase olive oil elaboration process i.e., olive washing water (OWW), olive oil washing water (OOWW), and olive mill solid waste (OMSW) in a closed-loop process. Initially, the microalga Raphidocelis subcapitata was grown using a mixture of OWW and OOWW as the culture medium, allowing phosphate, nitrate, sugars, and soluble chemical oxygen demand removal. In a second step, the microalgal biomass grown in the mixture of washing waters was used as a co-substrate together with OMSW for an anaerobic co-digestion process. The anaerobic co-digestion of the combination of 75% OMSW–25% R. subcapitata enhanced the methane yield by 7.0 and 64.5% compared to the anaerobic digestion of the OMSW and R. subcapitata individually. This schedule of operation allowed for integration of all of the byproducts generated from the two-phase olive oil elaboration process in a full valorization system and the establishment of a circular economy concept for the olive oil industry.