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The effect of particle size on physicochemical stability, bioaccessibility, and bioactivity of bioactive compounds is important in the design of delivery systems. It is challenging to control the size of delivery systems without altering chemical composition. In the present study, the re-assembly of dissociated egg yolk granules was modulated by Ca2+ to produce recombined granules with controlled hydrodynamic diameter (Dh). Quercetin was selected as a representative bioactive compound encapsulated within recombined granules (Gra-Que). Encapsulation efficiency and loading efficiency increased with an increase in Dh until phase separation occurred at 250 µg/mL Ca2+. The thermal and photochemical stability of Gra-Que increased as Dh increased, whereas samples with the smallest Dh demonstrated the highest storage stability. Gra-Que with an intermediate Dh had the highest bioaccessibility due to a balance between the protection of quercetin and susceptibility to digestion. Smaller samples had higher bioactivity due to higher cellular uptake and greater susceptibility to digestion.