<p>Given the green and tunable nature, ionic liquids have numerous industrial applications as potential alternatives to conventional intense inorganic/volatile organic solvents and costly instruments. In this study, six of 50 mM NH₄Cl, NaCl, KCl, MgCl₂, CaCl₂ or BaCl₂ were employed for extraction of phycobiliprotein-rich protein isolate (PRPI) from <i>Spirulina platensis</i> (<i>S. platensis</i>). It was demonstrated monovalent salts facilitated the extraction PRPI which differed in phycobiliprotein purity but all were found at the higher protein contents than those by divalent salts. In particular, protein subunit composition, structural properties and functionalities were significantly altered by the extraction ionic liquids. For instance, CaCl₂ or MgCl₂ extracted PRPI (PRPI_Ca²⁺ or PRPI_Mg²⁺) exhibited a larger percentage of beta-sheet and disulfide bonds as well as the promoted distribution of tryptophan on protein surface than the counterpart. Subsequently, PRPI_Ca²⁺ or PRPI_Mg²⁺ showed higher surface hydrophobicity/emulsifying stability but lower emulsifying ability. However, the PRPI_Ca²⁺ or PRPI_Mg²⁺, as by TGA analysis, showed lower thermal &amp; storage stability which was largely attributed to the highest phycobiliprotein purity when compared to its counterpart. Correlation analysis indicated that cation-induced changes in protein properties were closely linked to structural alterations, providing valuable data for future development of colloidal food systems.</p> Graphical Abstract <p></p>