This manuscript reveals the effect of the emulsification step on the black carrot extract (BCE) stabilization by potato protein isolate (PPI)-citrus pectin (CP) coacervates. The effect of core-to-wall ratio and concentration of wall material were also investigated. This was the first attempt to compare the characteristics of emulsified core particles (ECP) and non-emulsified core particles (NECP) coated with complex coacervates. Potato protein was used as an encapsulating agent by complex coacervation for the first time, and it showed excellent characteristics for the encapsulation. Non-hygroscopic particles were produced with emulsification while most of NECPs were slightly hygroscopic. The mean particle diameter of powders ranged from 65.05 to 152.47 μm which is suitable with SEM micrographs. ECPs showed lower particle size values with increased wall concentration at the constant core-to-wall ratio. Encapsulation efficiency (EE) increased, and anthocyanin retention (AR) decreased when emulsification was included. EE of NECP and ECP was between 69.26–82.84% and 85.48–90.15% while AR was between 79.08–102.16% and 53.90–83.37%, respectively. FT-IR and ζ-potential values proved the complexation between PPI and CP in ECPs as well as the interaction of PP, CP, and BCE in NECPs. DSC thermograms proved the success of the encapsulation procedure and thermo-stability of the BCE-loaded particles.