Two phenolic compounds, flaxseed polyphenol (FPP) and hydroxytyrosol (HT), were covalently adducted with flaxseed protein isolate (FPI) and then complex coacervated with flaxseed gum (FG). Flaxseed oil (FO) was microencapsulated using these complex coacervates as wall materials. The release of FO from these microcapsules and its digestion were studied using an in vitro digestion model. Most of the encapsulated oil (66–80%) was released in the intestinal stage, and 5–17% was released in the gastric stage. The proteolytic degradation of FPI from microcapsule shell and release of FO in the intestinal phase was slowed down by adduction to FPP but not to HT. The release of FO was highest (80%) in (FPI-HT)/FG/FO microcapsule, and 38.5% of released oil was lipolysed into free fatty acids. (FPI-FPP)/FG/FO microcapsules released the lowest amount of oil (66.3%) of which 28.9% was lipolysed. These findings suggest that the phenolic compound-adducted FPI/FG complex coacervates can be promising encapsulating shell materials that can remain intact in the gastric phase and deliver the encapsulant to intestinal phase.