This study aimed to improve the flavor of royal jelly residue via microencapsulation technology using Arabic gum and gelatin as wall materials. This microencapsulation technology showed a good encapsulation yield of 85.71 ± 2.84% and encapsulation efficiency of 92.34 ± 3.17%. The intact structures of the microcapsules were observed using optical and scanning electron microscopes. The results of the simulated gastrointestinal digestion proved that the microcapsules were well-tolerated in the gastric environment (a release rate of 32.95 ± 2.34%). Both electronic nose and electronic tongue evaluations showed that microencapsulation improved the sensory index of the royal jelly sieve residue. After microencapsulation, the astringency, bitterness, and irritant odors of the royal jelly residue were reduced. Simultaneously, the release rate in the intestine was 98.77 ± 1.91%, which demonstrated that microencapsulation would not prevent the human body from absorbing the royal jelly. The results from this study are expected to facilitate the development of mild flavor products made from royal jelly.