Alginate gels are outstanding biomaterials widely applicable in food and pharmaceutical industries. This contribution provides comprehensive insight into the design of advanced hybrid alginate/pectin co -networks double crosslinked by Ca2+/Zn2+ ions encapsulating self -emulsifying systems (SES). The tunable mucoadhesive properties, structural stability, integrity, dissolution profiles, and enhanced in -vivo bioavailability make the synthesized hybrid systems ideal vehicles for the delivery of lipophilic phytotherapeutics, allowing the long-term site -specific treatment of intestinal inflammation. This work also provides a thorough understanding of the structure -property relationships of alginate -pectin gels at the atomic resolution level. It was found out that SES molecules form well -distributed, phase -separated microparticles that interact with the polysaccharide matrix through a well-defined interface. The hybrid alginate -pectin gel is highly cross -linked, with both types of polysaccharides participating in the network formation. The observed surface interactions of SES droplets increase the intrinsic mobility of the network. The plasticizing effect can be regulated by the amount of pectin macromolecules, whose interaction with alginate chains enables a strengthening of the polysaccharide network. Overall, the domain -like architecture of hybrid alginate -pectin gels synthesized by external ionic gelation is revealed; the key structural motifs responsible for their properties are discovered; and the pathways allowing their regulation are identified. Biological in -vivo tests then confirmed positive effects of the synthesized systems in living organisms. The strategy presented thus offers a new perspective for the rational design of alginate -based materials for the microencapsulation of bioactive compounds for advanced orally administered delivery systems or controlled -release decontaminators applicable in the food and nutraceutical processing industries.