Chlorella sp. and Spirulina (Arthrospira) sp. account for over 90% of the global microalgal biomass production and represent one of the most promising aquiculture bioeconomy systems. These microorganisms have been widely recognized for their nutritional and therapeutic properties; therefore, a significant growth of their market is expected, especially in the nutraceutical, food, and beverage segments. However, recent advancements in biotechnology and environmental science have led to the emergence of new applications for these microorganisms. This paper aims to explore these innovative applications, while shedding light on their roles in sustainable development, health, and industry. From this state-of-the art review, it was possible to give an in-depth outlook on the environmental sustainability of Chlorella sp. and Spirulina (Arthrospira) sp. For instance, there have been a variety of studies reported on the use of these two microorganisms for wastewater treatment and biofuel production, contributing to climate change mitigation efforts. Moreover, in the health sector, the richness of these microalgae in photosynthetic pigments and bioactive compounds, along with their oxygen-releasing capacity, are being harnessed in the development of new drugs, wound-healing dressings, photosensitizers for photodynamic therapy, tissue engineering, and anticancer treatments. Furthermore, in the industrial sector, Chlorella sp. and Spirulina (Arthrospira) sp. are being used in the production of biopolymers, fuel cells, and photovoltaic technologies. These innovative applications might bring different outlets for microalgae valorization, enhancing their potential, since the microalgae sector presents issues such as the high production costs. Thus, further research is highly needed to fully explore their benefits and potential applications in various sectors.