In this research, complex coacervation between soy protein isolate (SPI) and gum arabic (GA) constituted a preliminary step for developing chia oil (CO)-in-water emulsions suitable for subsequent spray drying. The contributions of total biopolymer concentration, SPI-GA ratio w/w and ionic strength on coacervate yield (CY) were quantified through a 3×6×4 factorial design. The SPI-GA ratios that gave the highest CY values (1-1 and 2-1) were selected to prepare emulsions and blank dispersions (devoid of CO). The preparation process included four well-defined sequential steps: high speed homogenization, high pressure homogenization, complex coacervation and a carrier addition (maltodextrin). The emulsification step, the SPI-GA ratio and the presence of CO had a significant effect (p ≤ 0.05) on ζ-Potential, apparent viscosity, structural recovery of the systems, gel strength and cross-linking. The microencapsulation process preserved the quality of CO (2.18 ± 0.01 h), as reflected by enhanced oxidative stability indices (around three times higher than bulk CO, 5.65–6.84 h) and non-significant changes in α-Linolenic acid after spray drying and in-vitro digestion processes (60–66.53%, relative abundance). In addition, thermogravimetric analysis (TGA) and Fourier transform infrared spectroscopy (FTIR) helped corroborate the stability of CO within the powders' structure. Finally, different characteristics of powders were significantly influenced (p ≤ 0.05) by the presence of CO, especially the color, flowability and sorption-dependent properties: the monolayer content (Wm) and the bulk moisture diffusivity.