In the search for oils of commercial interest that serve as new sources for the generation of cosmetic, pharmaceutical, or nutraceutical products, the green coffee beans oil (Coffea arabica L.) was studied. This research aimed to evaluate the oxidative stability of microencapsulated green coffee oil (Coffea arabica) by spray drying. The green coffee oil emulsions were produced by microfluidization using mesquite gum and octenyl succinic anhydride modified starches (OSA-starch) as wall-material. The particle size, polydispersity, and zeta potential on the microfluidized emulsions were optimized. The results showed that microfluidization had positive effects on the reduction of the emulsion droplets and the zeta potential, developing stable emulsions for both polymers. Then, the optimal microfluidization conditions were used to evaluate the impact of the spray drying conditions on the microencapsulation efficiency, morphology, and oxidation stability of the green coffee oil microcapsules under accelerated storage conditions (32% relative humidity (RH) at 25 °C). The microencapsulation efficiency was approximately 98% for both wall-materials. The morphology of the microcapsules showed spherical shapes and polydisperse sizes, a typical characteristic of spray-dried powders. The oxidative stability of the microcapsules was lower than the bulk green coffee oil (87.39 meq of O2/kg of oil), reaching values of 60.83 meq of O2/kg of oil for mesquite gum and 70.67 meq of O2/kg of oil for OSA-starch. The microcapsules produced have good potential for the development of nutraceutical foods or cosmetic formulations with adequate stability.