Sour cherry (Prunus cerasus L.) seeds are obtained as byproducts of the processing of sour cherries into processed foods. Sour cherry kernel oil (SCKO) contains n-3 PUFAs, which may provide an alternative to marine food products. In this study, SCKO was encapsulated by complex coacervates, and the characterization and in vitro bioaccessibility of encapsulated SCKO were investigated. Complex coacervates were prepared by whey protein concentrate (WPC) in combination with two different wall materials, maltodextrin (MD) and trehalose (TH). Gum Arabic (GA) was added to the final coacervate formulations to maintain droplet stability in the liquid phase. The oxidative stability of encapsulated SCKO was improved by drying on complex coacervate dispersions via freeze-drying and spray-drying. The optimum encapsulation efficiency (EE) was obtained for the sample 1% SCKO encapsulated with 3:1 MD/WPC ratio, followed by the 3:1 TH/WPC mixture containing 2% oil, while the sample with 4:1 TH/WPC containing 2% oil had the lowest EE. In comparison with freeze-dried coacervates containing 1% SCKO, spray-dried ones demonstrated higher EE and improved oxidative stability. It was also shown that TH could be a good alternative to MD when preparing complex coacervates with polysaccharide/protein networks.