This study aimed to microencapsulate Cymbopogon citratus essential oil (CCEO) with spray drying using maltodextrin and gelatin. The effects of the operational conditions (inlet temperature (130–160 °C), CCEO concentration (5–15%), maltodextrin concentration (10–20%)) on the physicochemical stability and antioxidant and antibacterial activities of the CCEO microcapsules were determined. The CCEO microencapsulation process had yield and encapsulation efficiency values varying from 31.02 to 77.53% and 15.86–61.95%, respectively. CCEO microcapsules had antibacterial effects against Staphylococcus aureus and Escherichia coli with minimum inhibitory concentration varying from 10 to 20%, and total phenolic contents and antioxidant activities varying from 1632 to 4171.08 μg TE/g and 28.55–45.12 µg/g, respectively. CCEO microcapsules had average diameters varying from 5.10 to 10.11 µm, with spherical external structures without cracks and apparent pores. The best desirable process conditions for CCEO microencapsulation were process inlet temperature of 148 °C, maltodextrin concentration of 15%, and CCEO concentration of 10%. The results showed that CCEO microcapsules with increased stability and low degradation of active components can be prepared by spray drying using maltodextrin and gelatin with the production of microcapsules, which could be exploited as potential food preservatives.