Microalgae biomass is known as a promising sustainable source of bioactive compounds. Application of microalgae biomass in food and feed products requires information regarding storage stability and optimized storage conditions to minimize unwanted deterioration which downgrades the bioactive composition of microalgae biomass. In order to investigate the worsening of the nutritional quality of freeze dried biomass, a multifactorial storage experiment was conducted on a high EPA (eicosapentaenoic acid) Nannochloropsis salina biomass. The storage time (0–56 days), storage temperature (5, 20,and 40 °C and packaging conditions (under vacuum and ambient pressure)used as main factors. During the 56 days of storage, both time and temperature strongly influenced the oxidation reactions which result in deterioration of bioactive compounds such as carotenoids, tocopherols, and EPA. Lipid deterioration occurred both due to enzyme-induced lipolysis and autoxidation. Carotenoids and α-tocopherol contents decreased during storage, but may stillhave prevented EPA from higher oxidative deteriorations due to their powerful antioxidant properties. Oxidation reactions, which resulted in the creation of primary and secondary volatile oxidation products, occurred mainly at the first days of storage. The resulting volatile compounds(measured by head space gas chromatography-mass spectrometry) declined further until day 56, probably due o reaction with amino acids, or decomposition to low molecular weight tertiary oxidation compounds. Storage of microalgae at low temperature is more effective than vacuum packaging. Practical Applications: Microalgae are known as a sustainable source of bioactive compounds, and their industrial scale application is growing very fast. Application of microalgae biomass in food, feed, or cosmetics requires the knowledge of the optimum storage conditions to prevent the value-added compounds from deterioration. Results of this study improve our understanding of the chemical deterioration under different storage conditions and can help the producers/customers to extend the shelf life of microalgae biomass by choosing correct storage conditions.