The effects of high-energy fabrication methods, namely high-pressure homogenization (HPH) and ultrasonication (US), on physicochemical properties of flaxseed oil-in-water nanoemulsions (FNEs) containing clove essential oil (CEO) and/or pomegranate peel extract (PPE) were studied during storage at 4 and 25°C. Nanoemulsions with relatively similar average droplet size were prepared by HPH and/or US. An increase in droplet size was observed over time. Lower storage temperature and fabrication by US increased Ostwald ripening rate. Higher storage temperature and fabrication by US decreased the centrifugal stability of nanoemulsions. CEO revealed better antioxidant properties than PPE. The oxidative stability was evaluated by determining secondary oxidation products, and fatty acids profile. The absence of antioxidant, fabrication by US, and higher storage temperature decreased the oxidative stability of nanoemulsions. The results of this study might be helpful in controlling the oxidation of FNEs during long-term storage and in designing functional foods and beverages.