The molecular structures determine the physical properties of milk proteins and are important for the texture of many dairy-based foods. Bovine α-lactalbumin (α-LA) is a globular 123 amino acid Ca2+ binding milk protein. Modification with microbial Ca2+ independent transglutaminase (MTGase) was used to modify lysines and glutamines in holo and apo α-LA. At 30 °C no lysines or glutamines are modified in holo α-LA, whereas in apo α-LA lysines 13, 16, 108, and 114, and glutamines 39 and 43, are modified. At 50 °C lysines 13, 16, 108, and 114, but no glutamines, are modified in holo α-LA, whereas in apo α-LA lysines 5, 13, 16, 108, and 114, and glutamines 39, 43, 54, 65, and 117, are modified. The methods presented here offer the possibility to manipulate the availabilities of residues in α-LA to the MTGase reaction and enable the preparation of α-LA species with different degrees of modification and hence with different physical properties.