In this work, natural biopolymeric encapsulation structures were developed through the self-assembly of gelatin and ι-carrageenan in aqueous solutions. The interactions of this binary system and of a ternary system containing a polyphenol-rich extract were deeply explored for the development of intestinal delivery systems. The processing of the structures (extrusion vs. freeze-drying) greatly influenced release properties, explained by the specific interactions between gelatin and polyphenols, thus allowing for tuning the processing conditions depending on the desired target application. Release was further controlled by incorporating a divalent salt, giving raise to extract-loaded ι-carrageenan/gelatin capsules with adequate release profiles for intestinal targeted delivery. These results demonstrate the potential of exploiting biopolymer interactions for designing bioactive delivery systems using environmentally friendly processes which do not involve the use of toxic or harsh solvents or cross-linkers.