An alternative methodology using different protic ionic liquids (PILs), mechanical agitation and thermal heating was proposed to obtain phycobiliproteins from the Spirulina (Arthrospira) platensis microalgae. The PILs N-methyl-2-hydroxyethylammonium acetate (2-HEAA) protic ionic liquid; N-methyl-2-hydroxyethylammonium formate (2-HEAF) protic ionic liquid; the mixture of these protic ionic liquids (2-HEAA + 2-HEAF) (1:1, v/v) were synthesized and their performance as solvent was compared to a control (sodium phosphate buffer). The results showed that all PILs were efficient in the extraction of phycobiliproteins. The most suitable conditions were: temperature of 35 °C; pH 6.50 and ratio solvent:biomass 6.59 mL·g−1, using 2-HEAA + 2-HEAF as solvent after 150 min of extraction. The maximum concentrations of phycocyanin, allophycocyanin and phycoerythrin were 1.65 g·L−1, 1.70 g·L−1 and 0.64 g·L−1, respectively. The obtained phycobiliproteins presented a purification index around 0.50 and can be applied in cosmetics and foods. The phycobiliproteins obtained by extraction using 2-HEAA + 2-HEAF exhibited appreciable antioxidant activity, 61.1% of DPPH scavenging activity and 77.4% of H2O2 scavenging activity, at a concentration of 20 mg/mL.