Fractionation of powders by Pulse Spray Drying (PSD) may improve drying behaviour in fruit smoothies prepared with apple, orange, banana, and whey protein. The objective of this study was to determine whether cyclone-based fractionation via PSD yields smoothie powder fractions with distinct physicochemical and functional properties. The obtained fine and coarse powder fractions (FP and CP) and their quality differences were compared after rehydration (FPS and CPS). Most product was obtained as FP in the cyclone owing to its better fluidization behaviour, while CP was retained in the drying chamber due to its larger particle size, higher density, higher moisture content, and lower glass transition temperature. Both powder fractions could be readily rehydrated for consumption. CPS and FPS reached similar oxidation levels for 5-(Hydroxymethyl)furfural, available Lysine, vitamin C, and α-tocopherol. In contrast, CPS exhibited greater discolouration and lipid oxidation than FPS. Antioxidant status values (total phenolics and ABTS, DPPH, and FRAP antiradical scavenging activities) were up to 51.5% lower in CPS than in FPS. Fractionation via PSD facilitates smoothie powdering; however, fractions generated under distinct thermo-oxidative conditions may exhibit different oxidative stability. The powders should be evaluated before blending to ensure consistent quality. They may require separate packaging, storage, or handling.