The extraction and biorefining of value-added chemicals from bioresources using green solvents are among the key agenda of the circular bioeconomy. Herein we have developed a deep eutectic solvent (DESs) based biorefining approach for clean separation and purification of value-added Fucoxanthin, Chlorophyll, and Biosilica from a diatom microalgae, Thalassiosira andamanica. Several hydrophilic/hydrophobic (DESs) based on quaternary ammonium salt as hydrogen bond acceptor and organic acids and alcohols as hydrogen bond donors were synthesized and tested for microalgae biomass dissolution and biorefining via the phase partitioning method. In an optimized process, ∼30 wt% of fresh weight diatom could be dissolved in hydrophilic DESs at room temperature, followed by a record extraction of 19.93 mg/g of Fucoxanthin via phase partitioning, with a 53 % increase in yield and an 81 % increase in selectivity over conventional solvents. 1H NMR, FTIR, LCMS, UV, and HPLC techniques were used to characterize the extracted Fucoxanthin. Subsequently, a hydrophobic DES was added to the remaining hydrophilic DESs and residual biomass and Chlorophyll were extracted into the upper hydrophobic DES layer and Biosilica (80 mg/g) was recovered by simple centrifugation. Extracted Biosilica showed an excellent adsorption capacity of 224.71 mg/g for the removal of methylene blue (MB) dye from water (94.3% up to 88.8 % after 4th consecutive steps). Whereas Chlorophyll extracted in the hydrophobic DES phase exhibited excellent photostability (6 folds greater than conventional solvent) indicating the efficacy of DESs as photoprotector for light-sensitive pigments. This is the first report wherein besides an extractant DES also acted as a good photostabilizer. Additionally, we have replaced the acid-based extraction method for Biosilica with non-toxic DESs.