Essential oils (EOs) are widely used in various industrial sectors but can present several instability problems when exposed to environmental factors. Encapsulation technologies are effective solutions to improve EOs properties and stability. Currently, the encapsulation in lipid nanoparticles has received significant attention, due to the several recognized advantages over conventional systems. The study aimed to investigate the influence of the lipid matrix composition and spray-drying process on the physicochemical properties of the lipid-based nanoparticles loaded with Lippia sidoides EO and their retention efficiency for the oil. The obtained spray-dried products were characterized by determination of flow properties (Carr Index: from 25.0% to 47.93%, and Hausner ratio: from 1.25 to 1.38), moisture (from 3.78% to 5.20%), water activity (<0.5), and powder morphology. Zeta potential, mean particle size and polydispersity index, of the redispersed dried product, fell between −25.9 mV and −30.9 mV, 525.3 nm and 1143 nm, and 0.425 and 0.652, respectively; showing slight differences with the results obtained prior to spray-drying (from −16.4 mV to −31.6 mV; 147 nm to 1531 nm; and 0.459 to 0.729). Thymol retention in the dried products was significantly lower than the values determined for the liquid formulations and was affected by the drying of nanoparticles.