The conjugates of biomacromolecules such as proteins and polysaccharides have potential to stabilize the emulsion system and encapsulate valuable bioactive compounds for biofortification in food systems. In this study, native banana starch (NBS) was isolated from green culled banana and modified into resistant starch (type III) by lintnerization followed by autoclaving-cooling process, resulting in lintnerized-autoclaved banana starch (LABS). Soy protein isolate (SPI) was used for developing the polysaccharide-protein conjugates i.e. LABS-SPI conjugate and used as wall material to stabilize the oil-in-water emulsion system. LABS-SPI conjugate emulsions were subjected to in vitro digestion model and oxidative stability evaluation. Furthermore, the emulsion system was enriched with astaxanthin and evaluated for its stability. The chemical finger printing of LABS-SPI conjugates showed stretching in immine and enaminol group of Schiff's bases, the CN stretching of Amadori product. During in vitro digestion LABS-SPI conjugate emulsion showed that the presence of resistant starch had an influence on the droplet digestion process and significantly (p < 0.05) lower free fatty acid release compared to emulsions stabilized by SPI alone. LABS-SPI conjugate emulsion system demonstrated higher stability of astaxanthin at storage temperatures (6, 20 and 37 °C), and can be used for biofortification of food and pharmaceutical formulations.