In this work, several routes for obtaining high value pigments, fermentable sugars, crude algae oil and biodiesel were evaluated using the microalgae strain Amphiprora sp. in order to develop a topology of microalgae-based biorefinery. For chlorophylls and phycobiliproteins extraction, ethanol and methanol were evaluated as solvents, for reducing sugars production, Organosolv pretreatment (OSE), acid hydrolysis (HSE), and multifunctional systems using ethanol (MSE) and methanol (MSM) were compared. For lipid extraction, five solvent-based methods were compared with multifunctional process and for biodiesel production, transesterification, MSE and MSM were used. Results shows that several bioproducts can be obtained from Amphiprora sp. microalgae and can be a promissory strain for the development of a biorefinery, two routes were defined: one route without the use of multifunctional processes with includes pigments extraction using ethanol, reducing sugars production by organosolv pretreatment, lipid extraction by HBE method and oil transesterification by methanol/NaOH; and a second route composed by pigments extraction using ethanol, multifunctional process by MSE route and biodiesel production from algae oil by methanol/NaOH transesterification.