Whey protein microparticles are of great potential in diverse applications such as fat replacement, emulsification,cargo delivery and formulation of high-protein beverages. We developed a method by which the major whey protein, β-lactoglobulin, (β-lg) is at first encapsulated through a facile procedure within CaCO3 microtemplates, followed by enzymatic crosslinking of the protein and succeeding removal of the template to form protein microparticles. Protein encapsulation increased the colloidal stability and influenced the micro-morphology of CaCO3 microparticles. Dynamic light scattering and ζ-potential measurements, supported by gel electrophoresis indicated that β-lg was entrapped in monomeric form. Heating of the protein-loaded CaCO3 microparticles to gel protein as an alternative to enzymatic crosslinking, was not feasible because pH reduction to 7.0 before heating caused considerable agglomeration and deformation of the carbonate particles. In subsequent to enzymatic crosslinking and template dissolution, confocal laser scanning microscopy illustrated that the resulting protein particles were spherical, micron sized (≈3μ) and structurally homogenous. It was found based on Fourier transform infra-red spectroscopy that enzymatic crosslinking twisted the β-sheet structures of β-lg. Gel electrophoresis and intrinsic fluorescence measurement showed that in addition to the enzymatic polymerization, thiol-disulfide exchange reactions contributed in protein particles formation. It was also concluded based on intrinsic fluorescence measurement that tryptophan microenvironment was not influenced by the enzymatic crosslinking. The fabricated β-lg particles did not undergo significant denaturation by subsequent heating. This may open a route to deliver near-native whey protein microparticles to final consumers.