The objective of this study was to investigate for the first time the role of S. cerevisiae natural barriers and endogenous cytoplasmatic bodies on the stabilization of fisetin encapsulated via sonoprocessing coupled to freeze-drying (FD) or spray drying (SD). Both protocols of encapsulation improved the resistance of fisetin against thermal treatments (between 60 and 150 °C) and photochemical-induced deterioration (light exposition for 60 days) compared to non-encapsulated fisetin (antioxidant activity retention of approximately 55% and 90%, respectively). When stored under constant relative humidity (from 32.8 to 90%) for 60 days, yeast carriers improved the half-life time of fisetin by up to 4-fold. Spray dried particles were smaller (4.9 μm) and showed higher fisetin release after simulated gastrointestinal digestion (55.7%) when compared to FD. Freeze-dried particles, in turn, tended to agglomerate more than SD (zeta potential -19.7 mV), resulting in reduced loading features (6.3 mg/g) and less efficient protection of fisetin to heat, photo, and moisture-induced deterioration. Overall, spray-dried sonoprocessed fisetin capsules are an efficient way to preserve fisetin against harsh conditions. Altogether, this report shows that sonoprocessing coupled to drying is an efficient, creative, and straightforward route to protect and deliver lipophilic fisetin using yeast capsules for food applications.