Microalgae have been increasingly viewed as a sustainable “biofactory” with high potentials to cope up to the present and future needs of food and nutrition. Inclusion of polyunsaturated fatty acids (PUFAs): docosahexanoic acid (DHA) and ecosapentanoic acid (EPA), in organic food products such as infant formulas, baby foods, yogurts, fluid milk, and soy milk is a common practice in the fortification process of those products. However, the supply of PUFA is facing serious challenges nowadays, to meet the increasing market demand due to insufficient production by aquacultures compounded with population growth, global warming, and overfishing. Recently, PUFAs from microalgae are gaining attention with the hope that they substitute the omega fatty acids usually sourced from fish. However, the lack of cost-effective and environmentally friendly technologies for the downstream processing of PUFA production from microalgae is a major problem for industrial-scale production. This review presented the recent advances in drying and pretreatment of microalgae biomass, the drawbacks of conventional PUFA extraction methods, and the recent eco-friendly alternative technologies.