Fish oil-loaded brown and green macroalgae-based nanoliposomes (NS: Sargassum boveanum, NP: Padina distromatica, and NC: Caulerpa sertularioides) were successfully obtained. Release profile (<35%), zeta particles size (130.3–266.3 nm), encapsulation efficiency (99.9%) were revealed besides morphological characterizations (NS: 157.55, NP: 129.02, NC: 335.304 nm) of nanoliposomes (p < 0.05). Oxidation tests demonstrated that the use of NS more successfully limited the rapid increase in peroxide value of fish oil stored at 30 °C. FFA value of control group samples reached 6.8 from 3.4% (change: 100%) while NS (change: 12.5%) and NP (change: 12.5%) had better stability during 42 days' storage (p < 0.05). The anisidine values of control group samples were in the range of 8.8 and 22.8. But, NS, NP, and NC samples possessed 11.0, 9.9, and 10.0, respectively. Totox value in the control group fish oil samples reached 85.2. Yet, the highest values for NS, NP, and NC samples were found to be 33.1, 54.5, and 67.3 (p < 0.05). Also, color values in the samples treated with nanoliposomes had higher stability. The use of nanolioposme technique effectively retarded the oxidation in fish oil stored at 30 °C. Thus, this applied novel methodology provided with a nanoliposomal approach can guide further food treatments in the food industry.