BACKGROUNDNannochloropsis algae contain approximately 20% polyunsaturated fatty acids (PUFA) and hold significant potential for high‐quality eicosapentaenoic acid (EPA) food industrialization. However, EPA in Nannochloropsis sp. is prone to oxidation, and microbial growth is a critical factor affecting the shelf life of fresh food. Storage composition and temperature are primary factors influencing microbial growth, yet these aspects are not fully understood. This study investigates the effects of temperature and encapsulation on EPA content in nano‐products over time. Nano‐powder and nanobeads derived from Nannochloropsis sp. served as raw materials. Additionally, changes in aerobic plate counts and coliform groups were monitored.RESULTSThe results indicated that nanobeads, due to their more complex processing and less mature packaging, were more susceptible to coliform contamination compared to nano‐powder. In terms of EPA stability, nanobeads exhibited a longer storage life than nano‐powder. The oxidation rate of both nano‐powder and nanobeads was faster at 37 °C than at 25 °C.CONCLUSIONThese findings can inform general shelf life estimation, rapid detection of total lipid content in nano‐products and macro extraction of nano‐oil. Moreover, they have significant implications for delaying EPA oxidation in nano‐products and improving hygienic quality control for microbial detection. © 2024 Society of Chemical Industry.