The objective of this techno-economic analysis is to define the costs for an industrial microalgae production process, comparing different operation strategies (Nannochloropsis oceanica cultivation during the whole year or cultivation of two species, where Phaeodactylum tricornutum and Tisochrysis lutea alternate), production scales (1 and 10 ha), harvesting technologies (centrifugation or ultrafiltration) and drying methods (freeze-drying or spray drying). This study is based on an industrial scale process established in the south of Portugal. The strategy of cultivating N. oceanica all year round is more attractive from an economic perspective, with production costs of 53.32 €/kg DW and a productivity of 27.61 t/y for a scale of 1 ha, a 49.31% lower cost and two-fold productivity than species alternation culture strategy. These results are for biomass harvested by centrifugation (10.65% biomass cost) and freeze-drying (20.15% biomass cost). These costs could be reduced by 7.03% using a combination of ultrafiltration and spray drying, up to 17.99% if expanded to 10 ha and 10.92% if fertilisers were used instead of commercial nutrient solutions. The study shows potentially competitive costs for functional foods, food, and feed additives, specialised aquaculture products (live feed enrichment) and other high value applications (e.g., cosmetics).