This study investigated the production and characterization of a functional flavored milk fortified with shrimp-derived astaxanthin (ASX)-rich oil in free and nanoencapsulated (hexosomal) forms. ASX-rich oil was extracted from green tiger shrimp (Penaeus semisulcatus) processing by-products using supercritical CO₂ extraction and subsequently incorporated into food-grade hexosomes. The resulting ASX-loaded hexosomes exhibited a mean particle size of 164.3 nm, a polydispersity index of 0.29, and a ζ-potential of -36.5 mV. Encapsulation efficiency reached 85.1 ± 3.3%, demonstrating the effective incorporation of ASX-rich oil within the nanostructured lipid carriers. Fortified flavored milk samples were prepared using free and hexosomal ASX-rich oil and evaluated during 12 days of refrigerated storage (4 °C) in terms of physicochemical, rheological, color, and sensory properties. The hexosomal ASX-fortified samples showed pH and titratable acidity profiles comparable to the control, while samples enriched with free ASX exhibited a significantly greater pH decline and higher acidity. Apparent viscosity increased in fortified samples, particularly in those containing hexosomal ASX, reflecting enhanced structural interactions and dispersed phase contributions. Color analysis revealed that nanoencapsulation mitigated excessive increases in redness and yellowness, while maintaining higher lightness compared to free ASX-fortified samples. Sensory evaluation demonstrated that hexosomal encapsulation effectively masked undesirable fishy odor and preserved overall acceptability, whereas free ASX-fortified milk received significantly lower sensory scores. Overall, the results demonstrate that hexosomal nanoencapsulation is an effective strategy to improve the physicochemical stability, color quality, and sensory acceptance of flavored milk fortified with shrimp-derived ASX, highlighting its potential for developing value-added functional dairy products.