Quercetin (Q) is a flavonoid used as an antioxidant in nutritional supplements and functional foods. However, the hydrophobicity of quercetin limits bioaccessibility. Whey protein concentrate (WPC) has amphiphilicity and high bio-compatibility with low-cost. However, the bioaccessibility of WPC-Q has not been studied systematically. Therefore, a quercetin-loaded delivery system was developed using WPC. The interactions between WPC and quercetin were investigated by molecular docking and fluorescence resonance energy transfer, and the solubility and bioaccessibility of quercetin in spray- or freeze-drying complexes. Storage stability and electronic tongue bitterness evaluation were assessed. Quercetin bound the hydrophobic amino acids of WPC through hydrophobic interactions, and was significantly increased the encapsulation efficiency and solubility (61.7% and 0.047 g/L) when binding to WPC preheated at 80 °C for 30 min (80WPC). The particles were more uniform and the dissolution ratio of quercetin was higher (80%–84% vs. 86%–94%, except for isoelectric points) for freeze-dried than spray-dried samples, so that higher quercetin retention in the digestive juice (76.0% vs. 64.1%) and easier digestion were obtained with freeze-dried powders. The drying method did not modify the antioxidant properties of the complexes in the digestive fluids. The digested proteins still protected quercetin from degradation in the intestinal fluids. The 80WPC-Q complexes in a dry state could maintain the stability of quercetin and mask its bitterness.