Maillard reaction based protein-polysaccharide conjugates (PPC) are typically better emulsifiers than the proteins used to form them. Such conjugates have been proposed as encapsulation agents, but their potential as nanoencapsulation agents in clear beverages has not yet been proposed. In this research we formed casein-maltodextrin (CN-MD) conjugates and co-assembled them with hydrophobic nutraceuticals to create nanovehicles for the enrichment of clear beverages. Conjugation was validated using gel electrophoresis and by ortho-phthaldialdehyde (OPA) assay. Vitamin D (VD) was nano-entrapped by the conjugates, and compared to controls based on an unconjugated CN-MD mixture and unencapsulated VD. The following advantages of the conjugates were shown: the diameters of conjugate-VD nanoparticles was smaller and their solution was more transparent than that of the vitamin dispersion or the protein-polysaccharide mixture with VD. Conjugates conferred better protection against oxidation to both VD and epigallocatechin gallate (EGCG) than the CN-MD mixture. Conjugates were more colloidally stable at the CN original pI, allowing the formation of nanoparticles with mean diameter below 30 nm when mixed with VD, even at the original pI of CN. Conjugates provided protection against degradation at low pH and during shelf life. Entrapment efficiency was measured using Nile red (NR), a fluorescent model for a hydrophobic nutraceutical. Protein affinity to the hydrophobic compound was not diminished due to conjugation, and 90% entrapment efficiency was obtained under the conditions tested. During simulated gastric digestion, Nile red was not released from the conjugates, suggesting potential application in enteric delivery.