Microalgae are often called “sustainable biofactories” due to their dual potential to mitigate atmospheric carbon dioxide and produce a great diversity of high-value compounds. Nevertheless, the successful exploitation of microalgae as biofactories for industrial scale is dependent on choosing the right microalga and optimum growth conditions. Due to the rich biodiversity of microalgae, a screening pipeline should be developed to perform microalgal strain selection exploring their growth, robustness, and metabolite production. Current prospects in microalgal biotechnology are turning their focus to high-value lipids for pharmaceutic, nutraceutic, and cosmetic products. Within microalgal lipid fraction, polyunsaturated fatty acids and carotenoids are broadly recognized for their vital functions in human organisms. Microalgal-derived phytosterols are still an underexploited lipid resource despite presenting promising biological activities, including neuroprotective, anti-inflammatory, anti-cancer, neuromodulatory, immunomodulatory, and apoptosis inductive effects. To modulate microalgal biochemical composition, according to the intended field of application, it is important to know the contribution of each cultivation factor, or their combined effects, for the wanted product accumulation. Microalgae have a vital role to play in future low-carbon economy. Since microalgal biodiesel is still costly, it is desirable to explore the potential of oleaginous species for its high-value lipids which present great global market prospects.