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This work explores the efficiency of supercritical fluid extraction (SFE) to recover minerals, pigments, and antioxidant compounds from the spirulina microalgae. Moreover, the fatty acids and phenolic profiles of the extracts obtained were also investigated, and the effect of the extracts on SH-SY5Y cell viability was tested. The extraction of phycocyanin was improved by SFE compared to conventional extraction, from 2.838 ± 0.081 mg/g dry matter (DM) (control) to 6.438 ± 0.411 mg/g DM (SFE). SFE treatment also improved chlorophyll a and carotenoid recoveries increasing from 5.612 ± 0.547 to 8.645 ± 0.857 mg/g DM and from 0.447 ± 0.096 to 0.651 ± 0.120 mg/g DM, respectively. Regarding minerals, the SFE improved Mg recovery with 77% more than the control extraction. Moreover, palmitoleic, stearic, γ-linolenic, eicosadienoic and eicosatrienoic acids recovery was improved by SFE. Phenolic profiles were identified via triple-TOF-LC-MS-MS. Considering heavy metals, a higher rate of Pb extraction was observed for the SFE extract, while no significant differences were observed for Hg between both extractions. Finally, SFE extract improved cell viability compared to the control extract. Thus, SFE constitutes an interesting tool to sustainably extract high-added-value compounds; however, potential contaminants such as Pb need to be controlled in the resulting extracts.