Two bioactive compounds, quercetin and ferulic acid, were encapsulated using the electrospinning technique within hybrid amaranth protein isolate (API):pullulan ultrathin fibers. Initially, the composition of the encapsulation structures was optimized, both in terms of matrix components ratio and to maximize the bioactive loading. The morphology and thermal stability of the developed encapsulation structures were evaluated, as well as the encapsulation efficiency and distribution within the fibers of both antioxidant compounds. Moreover, the release characteristics and protection ability of the encapsulation structures during an in-vitro digestion study were investigated. Smooth ultrathin electrospun fibers were obtained in which the antioxidants were homogeneously distributed. Through this methodology, it was possible to incorporate within the API:pullulan fibers up to 10 and 20% (by weight) of quercetin and ferulic acid, respectively, which were released in a sustained manner during in-vitro digestion, keeping to a greater extent their antioxidant capacity in comparison with the non-encapsulated compounds.