Sustainability, at present, is a prominent component in the development of production systems that aim to provide the future energy and material resources. Microalgae are a promising feedstock; however, the sustainability of algae-based production systems is still under debate. Commercial market volumes of algae-derived products are still narrow. The extraction and conversion of primary metabolites to biofuels requires cultivation at large scales; cost-effective methods are therefore highly desirable. This work presents a complete and up to date review on sustainability analysis of various microalgae production scenarios, including techno-economic, environmental, and social impacts, both in large-scale plants for bioenergy production and in medium-scale cultivars intended for the production of high added-value chemicals. The results show that further efforts in algal-based research should be directed to improving the productivity, the development of multi product scenarios, a better valorization of coproducts, the integration with current industrial facilities to provide sustainable nutrient resources from waste streams, and the integration of renewable technologies such as wind energy in algae cultivars.