In this study, lutein and lycopene were encapsulated in plant protein (faba bean protein concentrate, (FPC))-carrageenan (Car) conjugates prepared by Maillard reaction in an aqueous media. The conjugation improved encapsulation yield that reached to 82.69% and 93.07%, for lycopene and lutein, respectively. The mean particle diameters for lutein loaded nanoparticles observed smaller in FPC-Car conjugates (66.60 nm) than FPC (71.49 nm). Scanning electron microscopy images showed that FPC-Car conjugates were more spherical and no fractures or fissures on the surface, revealing that wall materials provided better protection and retention for core materials. The diameter of lycopene nanoparticles coated with FPC remained constant between pH 3–4 and 7–9 but increased to 220 nm at pH 4–6. Even though the diameter of lutein nanoparticles coated with FPC remains steady between pH 5 and 9, increased to 953 nm at pH 3. The bioaccessibility of the lutein or lycopene samples encapsulated by FPC were found as higher than FPC-Car conjugates. These findings suggest that protein-polysaccharide conjugates could be used as a wall material to encapsulate lipophilic lutein and lycopene in order to improve their stability, property and bioaccessibility. As a result, FPC-Car conjugates may be an alternative for the formation of functional beverages as well as other nutraceutical products.