The use of polyphenols for enhancing protein function in the food industry is limited by their low bioavailability and stability. In this study, we developed complexes of the polyphenol pterostilbene (PTE) and goat lactoferrin (GLF) with the aim of developing a nutritionally enhanced food base with improved functional properties. Specifically, we investigated the binding affinity, structure, and functional modifications of PTE encapsulated with GLF. Fluorescence spectroscopy revealed notable changes in GLF, characterized by reduced fluorescence intensity and a blue shift in the emission peak, following interaction with varying concentrations of PTE. Fourier transformer infrared spectroscopy demonstrated a decrease in β-sheet content and an increase in β-turn structure with increasing PTE level. These structural alterations were furthered confirmed through molecular docking and molecular dynamics simulations. Furthermore, GLF–PTE complexes exhibited improved surface hydrophobicity, foaming capability, and emulsifying activity properties. Importantly, GLF maintained the antioxidant capacity of PTE under UV light irradiation and improved the bioaccessibility of PTE according to in-vitro intestinal digestion simulation assays. Furthermore, the GLF–PTE complexes showed no significant cytotoxicity to mouse fibroblast-like, goat mammary epithelial, or human kidney epithelial cells. This study elucidates the interaction mechanisms between GLF and PTE and supports the potential application of GLF–PTE complexes in food systems owing to their enhanced functional properties and bioactivity.