In milk, caseins interact to form nanoparticles called casein micelles. Under weak alkaline conditions, casein micelles swell reversibly and are disrupted at pH values above 8.5. The enzyme microbial transglutaminase (mTG) is widely used in food industry to modify the functional properties of proteins. Here, we evaluated the potential of mTG as a stabilizer for alkaline disrupted casein micelles. Hence, enzymatic cross-linking of casein micelles as well as sodium caseinate was studied at the natural milk pH 6.8 and under alkaline conditions at pH 7.9 by analyzing oligomerization via size exclusion chromatography, monomeric caseins via RP-HPLC-UV, and extra-micellar protein via Bradford assay. Additionally, alkaline swelling as well as enzymatic reconstruction of casein micelles was observed via scanning electron microscopy and dynamic light scattering. The results showed that the extent of cross-linking is mainly influenced by protein conformation and not by pH value. However, micellar alpha(s2)-casein was much more cross-linked at pH 7.9 compared to pH 6.8, whereas an opposite tendency was determined for micellar kappa-casein. This leads to the conclusion that a(s2)-casein is mainly located in the inner center of casein micelles and is only accessible for enzymatic cross-linking after alkaline swelling of the micelle. Alkaline disrupted casein micelles are reassembled due to intramicellar cross-linking by mTG. On the basis of the results, an enhanced model of the structure of casein micelles was developed.