The present work focuses on astaxanthin (ASX) extraction from shrimp wastes using ultrasound-assisted (UAE) natural deep eutectic solvents (NaDESs) and the utilization of ASX-rich NaDES extracts (ASX-NaDESs) for preparing biodegradable active packaging. The effects of hydrogen bond donor (HBD)/acceptor (HBA) molar ratio, ultrasound amplitude, extraction time for the ASX extraction were observed, and influential parameters were optimized using three-level-factor Box-Behnken design (BBD) with response surface methodology (RSM). The ASX-NaDES extract obtained in the optimum condition (68.98 ± 1.22 μg ASX/g shrimp waste), which was predicted by the model (69.09 μg/g of waste), was further used as plasticizer for chitosan (CS)-based biodegradable films. Films prepared using the ASX-NaDES/CS showed better radical scavenging activities than films prepared using pure NaDES/CS. Thermal stability, optical, and mechanical properties of the prepared films were also observed. ASX extraction using UAE NaDESs and further utilization of the ASX-NaDES extracts in biodegradable films can play an important role in cleaner production.