Bioactive compounds, such as curcumin, lutein, coenzyme Q10, β-carotene, cholecalciferol, astaxanthin, and β-sitosterol, have antioxidant and anti-inflammatory properties that promote health, but their low solubility, fast metabolism, and degradation have made it difficult to fully harness their potential. Encapsulation techniques, such as nano and microencapsulation using food-based biopolymers, have been employed to address these challenges. However, research efforts in protein-based delivery have mainly focused on encapsulation without considering structural, physicochemical, and matrix compatibility, which is tedious, unsustainable, and not cost-effective. Hence, this thesis reports the structural basis of guest-host interaction in the gastrointestinal delivery of lipophilic bioactive compounds using protein-based vehicles. This research employed fluorescence quenching techniques to estimate the influence of protein modification, fractionation and ionic strength on the nature and strength of interactions between protein and bioactive compounds. Morphological examination was carried out with transmission electron microscopy, confocal and widefield fluorescence microscopy whereas the sizes of the nano and micro-complexes was measured with dynamic light scattering techniques. Thermal stability was measured with differential scanning calorimetry and functional group characterization done with Fourier Transform infrared spectroscopy. Encapsulation efficiency was estimated by UV-Visible spectroscopy whereas in vitro bioactive compound release study was carried out in simulated salivary, gastric and intestinal fluids. Cytotoxicity assessment was estimated by calcein leakage assay. The study showed that protein modification affects the strength of protein-curcumin interaction and encapsulation efficiency. Pea protein succinylation increased electrostatic interaction with chitosan but decreased protein-curcumin interaction. Pea glutelin, albumin and globulin fractions showed different binding strengths with curcumin and the protein hydrophobicity and encapsulation efficiency correlated positively with the binding strength. The study also investigated the impact of bioactive compound lipophilicity and physiological ionic strength on the interaction between protein and bioactive compound. Lipophilicity influenced the strength of protein-bioactive compound interaction, while ionic strength changed the mode of interaction from static to static-dynamic quenching. The morphology of the nano and micro complexes formed with protein varied depending on the nature of encapsulated bioactive compound. Finally, bio-nano interaction involving giant unilamellar vesicles and curcumin-loaded pea protein of various surface functionalities as model biomembrane and nanoparticles respectively, was investigated. The result showed that while the protein/chitosan shell stabilizes bioactive compounds from degradation, the bioactive compound modulates their interaction with biomembrane. Overall, this work has demonstrated that for a rational design of protein-based nano/micro-encapsulation system, it is essential to consider the influence of the structural and physicochemical properties of proteins and bioactive compounds, stabilizing intermolecular forces, ionic strength of the environment, lipophilicity of the bioactive compounds, mechanism of release and modulation of cytotoxicity by bioactive compound. For instance, in high ionic strength solution, the stoichiometric ratio between protein carrier and bioactive compounds influences the stability of the complex. Balancing the intermolecular forces in the shell and core of bilayer complexes is essential for the stability of nanocomplexes and the presence of bioactive compound stabilizes the macromolecular carrier to minimal biomembrane disruption.