Many bioactive compounds are hydrophobic materials that are crystalline at ambient and body temperatures, which reduces their bioavailability and poses challenges to their successful incorporation into pharmaceuticals and functional foods. The aim of this study was to determine whether a hydrophobic crystalline bioactive component (quercetin) could be successfully incorporated into nanoemulsion-based delivery systems, and to evaluate the extent to which these delivery systems altered its bioaccessibility. The maximum amount of soluble quercetin that could be loaded into a carrier oil phase (medium chain triglycerides, MCT) at ambient temperature was C_Sat ≈ 0.15 mg mL⁻¹. At quercetin concentrations <C_Sat, nanoemulsions remained stable throughout 30 days storage at 5, 20 and 37 °C, i.e., no droplet growth, droplet creaming, or crystal formation were observed. At quercetin concentrations >C_Sat, nanoemulsions remained physically stable (no droplet growth or creaming), but quercetin crystals formed in the samples during storage. The bioaccessibility of quercetin was determined using an in vitro digestion model simulating the mouth, stomach, and small intestine. A higher percentage of quercetin was solubilized in the micelle phase after small intestine digestion when it was incorporated in nanoemulsions than when it was dispersed in either bulk oil or pure water. The bioaccessibility of crystalline quercetin was less than that of dissolved quercetin. The knowledge gained from this study is valuable for the rational design of delivery systems to incorporate crystalline hydrophobic bioactive compounds into pharmaceuticals and functional foods, and to increase their bioaccessibility.