This study presents a new cyanobacterium of the genus Geitlerinema sp. isolated from the Chilean coastal desert as a rich source of bioactive compounds. Phylogenetic tree is shown along with a broad biochemical characterization using conventional and pressurized liquid extraction. Variables as extraction yield, phycobiliproteins, lipids and methyl palmitate (C16:0) were studied by means of two experimental designs based on a response surface methodology (RSM) employing two factorial design 32. Factors as temperature (20–200 °C) and percentage of solvents were selected resulting in Factorial Design A with 0–100% (v/v) of ethanol–water and Factorial Design B with 0–100 (v/v) of ethanol–limonene solvents. The main bioactive compounds were total proteins (∼52% wt), phycobiliproteins (especially C-phycocyanin) and methyl palmitate (C16:0). Data obtained showed that water and ethanol:water (1:1, v/v) improved the extraction yield and phycobiliproteins recovery. As for ethanol:limonene extracts, they were better for lipids and methyl palmitate extractions. In general, high temperatures only improved the extraction yield whereas low temperatures favor the extraction of phycobiliproteins. Therefore, results indicated that Geitlerinema sp. could be one of the several cyanobacteria genera that display functional properties for nutritional, pharmaceutical or industrial use as sustainable and cost-effective bioactive compounds in algal biorefinery model. This work was supported by public funds of Chile such as MINEDUC-UA (grant number ANT-1855), Regional Government of Antofagasta (grant number FIC-R-30488815-0) and ANID (grant numbers FONDECYT-11170017 and PAI-79160037) and under project ABACUS (Algae for a Biomass Applied to the produCtion of added value compounds — funded by the Bio Based Industries Joint Undertaking under the European Union’s Horizon 2020 research and innovation programme under grant agreement No 745668). Peer reviewed