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BACKGROUND: Rutin is a natural bioactive flavonoid that is poor in water solubility and chemical stability. Encapsulation can be used to protect bioactive molecules from chemical or physical decomposition during food processing and storage. Thus, the effect of initial particle size on the ability of oil‐in‐water emulsions to retain rutin during storage was investigated. RESULTS: Rutin was encapsulated in oil‐in‐water emulsions with different mean surface‐weighted diameters: d3,2 = 0.56 μm (small), 0.73 μm (medium), and 2.32 μm (large). As expected, the resistance of the emulsions to coalescence and creaming during storage increased as the particle size decreased due to weakening of the colloidal and gravitational forces acting on the droplets. The concentration of rutin in the emulsions decreased during storage (28 days), which was mainly attributed to photodegradation of the flavonoid. The loss of rutin from the emulsions during storage was fitted using a second‐order equation. The rutin degradation rate constant k decreased and the half‐life t1/2 increased with decreasing droplet size, which was attributed to the stronger encapsulation and light scattering by smaller oil droplets reducing the amount of light that can penetrate into the emulsions. CONCLUSION: This study has important implications for the design of more efficacious emulsion‐based delivery systems for incorporating health‐promoting nutraceuticals into foods. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]