Arrowroot starch (AS), extracted from a tropical rhizome (Maranta arundinacea), was investigated and compared to maltodextrin (MD) in whey protein (WP) combinations for its potential as a novel wall material to microencapsulate and limit oxidative rancidity of tuna fish oil. Tuna fish oil was mixed into six emulsions composed of 5:1, MD:WP (P1); 6.5:1, MD:WP (P2); 5:1, AS:WP (P3); 6.5:1, AS:WP (P4); 3.344:1.668:1, MD:AS:WP (P5); and 3.25:3.25:1, MD:AS:WP (P6) to produce microcapsules by freeze drying. The microcapsules were studied for encapsulation efficiency (EE), moisture content, water activity, peroxide value (PV), acid value (AV), microstructure, and the degree of primary oxidation was evaluated every 15 days for 90 days at ±25 °C. The fish oil microcapsules demonstrated high EE (80.5–86.4%), low moisture content (0.24–3.47%), and low water activity (0.05–0.23). The microcapsules exhibited PV (4.80–9.20 mEq/kg oil) and AV (1.46–2.24 %FFA) values that remained below industry-set maximum limits of PV (10 mEq O2/kg oil) and AV (<3) for refined fish oil. Particle size of the freeze-dried microcapsules ranged 26.72–103.14 μm with irregular to smooth surfaces. Microcapsules of MD:AS:WP (P6) combination exhibited the highest oxidation stability during the 90-day storage test. The results demonstrated that arrowroot starch: maltodextrin combinations successfully encapsulated tuna fish oil, improved shelf life, and demonstrated oxidative stability. Moreover, arrowroot starch behaved as a cryoprotectant during freeze-drying, and as wall material in tuna fish oil microencapsulation indicated its microencapsulation carrier and application potential in food fortification.