Microalgae, as some of the oldest life forms on Earth, are of significant interest to industry and in terms of environmental policies, due to their ability to perform photosynthesis and consume atmospheric carbon dioxide. Moreover, they contain a wide variety of value-added compounds such as amino acids and proteins, carbohydrates, and fatty acids, which can be exploited in multiple fields like medicine, cosmetics, nutritional supplements, and for the production of biodiesel. In this article, Nannochloropsis gaditana, a type of microalgae that inhabits both fresh and salt water, is studied for fatty acid recovery using deep eutectic solvents (DES). This microalgae species is a natural source of eicosapentaenoic acid (EPA), an omega-3 compound that is commonly used in the nutritional industry. There are numerous extraction techniques and pretreatments to obtain these compounds. In this work, DES are studied as extractive agents due to their advantages as neoteric solvents. Specifically, this work focuses on an assessment of the effect of the composition of DES on the extraction yield of fatty acids from microalgae. Several DES compositions based on choline chloride, ethylene glycol, and fructose are studied to analyze the influence of water content in these phases. The results show that water content significantly influences recovery yields. The DES with higher extractive capacity were those based on choline chloride, ethylene glycol, and water at a molar ratio of 1:2:2. This composition offered 48.7% of the yield obtained with a conventional solvent like methanol for the recovery of EPA (11.2 mg/g microalgae). Furthermore, the choline chloride-fructose-based DES shows the capability of selective extractions of fatty acids with low carbon content—choline chloride:fructose:water (molar ratio 2:1:2) can extract 0.14 mg of decanoic acid/g of microalgae, indicating that this DES composition can recover 35.7% more decanoic acid in comparison to methanol.