Valorization of food industry waste and plant residues represents an attractive path towards obtaining biodegradable materials and achieving “zero waste” goals. Here, melanin was isolated from watermelon (Citrullus lanatus) seeds and used as a modifier for whey protein concentrate and isolate films (WPC and WPI) at two concentrations (0.1% and 0.5%). The modification with melanin enhanced the ultraviolet (UV) blocking, water vapor barrier, swelling, and mechanical properties of the WPC/WPI films, in addition to affecting the apparent color. The modified WPC/WPI films also exhibited high antioxidant activity, but no cytotoxicity. Overall, the effects were melanin concentration-dependent. Thus, melanin from watermelon seeds can be used as a functional modifier to develop bioactive biopolymer films with good potential to be exploited in food packaging and biomedical applications.