Bio-refining of algal biomass is currently considered as a key strategy to cut down the cost and improve the overall feasibility of algal-derived biodiesel. With that aim, in this study it was implemented a three-stage biorefinery process for the recovery of five differentiated bio-products from heterotrophically Chlorella protothecoides biomass. In the first stage, which was conducted at pilot scale from 14 kg of wet biomass, direct saponification converted 40% of dry algal biomass into free fatty acids. The obtained fatty acids were successfully turned into high quality biodiesel, whereas the analysis of unsaponifiables revealed the presence of interesting high-value biomolecules such as sterols (62%), squalene and carotenoids (1.7% each). The de-oiled biomass underwent an enzymatic hydrolysis process. This second process led to the valorization of 9% (0.09 kg/kg) of the remaining algal components which were recovered in a liquid hydrolysate mainly composed of soluble amino acids (15 g/L) and sugars (27.9 g/L). In the last biorefinery stage, the leftover solid fraction after enzymatic hydrolysis (0.36 kg/kg) was used as substrate in an anaerobic digestion process which yielded biogas at 196 ± 4 NL CH4/kg VS. The digestate co-produced in this stage was chemically characterized and assessed as fertilizer (at a dose of 170kg N/ha) for wheat and tomato plant growth, with comparable effect to that of industrial fertilizers. This use allowed a closed-loop system through the recycling of nutrients for primary production. The exposed cascade-processing, which was demonstrated technically feasible, could potentially improve the value of algal biomass through the production of multiple products.