Effective and controlled use of cross-linking enzymes in structure engineering of food systems depends on characterization of the favorable conditions for enzyme-substrate complex and the limiting factors for the desired modification. In this respect, we analyzed the susceptibility of bovine β-lactoglobulin (BLG) to enzymatic cross-linking by Trichoderma reesei tyrosinase (TrTyr) and transglutaminase (TG). Changes in BLG molecular structure were determined at pH 6.8, 7.5 and 9.0 before and after high-temperature heat treatment. The conformational change was linked to efficiency of protein cross-linking. BLG was not susceptible to TrTyr without heat treatment. TG, however, induced inter-molecular cross-links at pH 7.5 and 9.0. After the heat treatments, BLG molecules adopted a molten-globule-like conformation. Both of the enzymes were able to form inter-molecular cross-links between heat-denatured BLG molecules. Electrophoretic mobility and broadness of the oligomer bands created by both enzymes on SDS-PAGE gels showed differences which were linked to the availability and number of target amino acid residues. Evidence for intra-molecular cross-linking was obtained. Once adsorbed to air/water interface, BLG formed a viscoelastic surface film which was characterized by surface shear rheology. Application of cross-linking enzymes under a dense layer of BLG molecules at the interface led to decreasing G′ with time. Intra-molecular links were most probably favored against inter-molecular on packed BLG layer leading to constrained molecules. Results in general emphasize the importance of structural and colloidal aspects of protein molecules in controlling inter/intra-molecular bond formation by cross-linking enzymes.