Polyphenols are widely known for their benefits to human health; however, dietary intake of this class of compounds is low in the United States due to low intake of fruits and vegetables. Dairy foods (i.e., milk, yogurt) have been shown to increase polyphenol bioavailability via protein–polyphenol interactions, which may have important implications for human health. Increasing consumer interest in sustainability and health has led to the introduction of a variety of novel plant-based proteins and related food products as dairy alternatives. This study compared whey, a popular dairy-based food protein, to pea and hemp proteins for their abilities to form complexes with polyphenols from blueberries, which are a widely consumed fruit in the US with demonstrated health effects. Physical and chemical characteristics of each protein extract in the presence and absence of blueberry polyphenols were investigated using a variety of spectroscopic methods. The influence of polyphenol complexation on protein digestion was also assessed in vitro. While all proteins formed complexes with blueberry polyphenols, the hemp and pea proteins demonstrated greater polyphenol binding affinities than whey, which may be due to observed differences in protein secondary structure. Polyphenol addition did not affect the digestion of any protein studied. Solution pH appeared to play a role in protein–polyphenol complex formation, which suggests that the effects observed in this model food system may differ from food systems designed to mimic other food products, such as plant-based yogurts. This study provides a foundation for exploring the effects of plant-based proteins on phytochemical functionality in complex, “whole food” matrices, and supports the development of plant-based dairy analogs aimed at increasing polyphenol stability and bioavailability.