An in vivo study using the nematode Caenorhabditis elegans explored the benefits of a whey protein hydrolysate (WPH), derived from cheese whey through a novel enzymatic process. In this model, WPH demonstrated significant hypolipidemic, antioxidant, and neuroprotective qualities. Nematodes fed with a WPH diet displayed substantial reductions in body fat (20.8%, p < 0.001), triglyceride (29.3%, p < 0.05), and cholesterol levels (28.9%, p < 0.01) compared to controls. Under oxidative stress, WPH-fed nematodes had a 27% better survival against hydrogen peroxide. In a specific transgenic C. elegans strain with Aβ peptide induction, 400 μg mL-1 of WPH led to only 47.1% paralysis 30 hours post-induction, versus 100% in controls. This study paves the way for the development of targeted functional foods or supplements addressing health issues such as high cholesterol, oxidative stress, and neurodegeneration, providing a scientific foundation for their future formulation.