Spray drying (SD) is widely used for fruit powder production, but hygroscopic compounds can affect flowability and cause stickiness. This study evaluated rice protein and rice starch as encapsulating agents during SD of blueberry pulp (BPP and BPS, respectively), combined with ozone aeration (BPP-O3 and BPS-O3), focusing on physical, morphological, structural, and bioactive properties, as well as 56-day stability. The process yield was 55.26% (BPP) and 52.5% (BPS) (p < 0.05). All microparticles had low moisture (<5.03%) and water activity (<0.21%). BPP had higher phenolic (308.60 mg GAE/100 g) and anthocyanin content (85.26 mg/100 g), while BPS had more flavonoids (33.84 mg CE/100 g). Ozone treatment increased solubility (89.10–91.27%) and reduced hygroscopicity (9.25–10.06%). Morphological analysis revealed that BPP produced smaller, uniform particles (11.70 µm), whereas BPS generated larger (16.67 µm) and more agglomerated particles. Ozone improved sphericity, reduced agglomeration, and enhanced flow properties. FT-IR analysis indicated no new functional groups but a reduction in absorbance bands. Ozone also enhanced the stability of bioactive compounds, reducing anthocyanin and flavonoid degradation over 56 days. Overall, BPP-O3 is a promising approach for producing functional powders with enhanced stability and physical properties, suitable for food applications.