The growing demand for molecules of interest from microalgal biomass, such as phycobiliproteins, has led to an accumulation of unused by-products. For example, phycocyanin, obtained by the extraction of Spirulina, generated cakes rich in non-polar molecules of interest, such as free fatty acids (FFAs). These FFAs were generally considered as markers of lipidome degradation, but represented a relevant alternative to topical antibiotics, based on a biomimetic approach. In order to develop a sustainable Spirulina biorefinery scheme, different pretreatments and alternative solvents were screened to identify the best combination for the valorization of FFAs. Thus, five pre-treatments were studied including a phycocyanin extraction by-product. The following three biobased solvents were selected: ethyl acetate (EtOAc), dimethyl carbonate (DMC) and a fatty acid-based natural deep eutectic solvent (NaDES). The pigment and fatty acid profiles were established by spectroscopic and chromatographic approaches. NaDES demonstrated superior extraction capacity and selectivity compared to other biobased solvents, regardless of pretreatment. In contrast, EtOAc and DMC showed a greater diversity of FFAs, with a predominance of polyunsaturated fatty acids (PUFAs). The by-product has also been highlighted as a relevant raw material facilitating the recovery of FFAs. These results pave the way for a green biorefinery of the lipid fraction and phycobiliproteins of microalgae.