The essential amino acid lysine plays an important role for the nutritional quality of infant formula. Unfortunately, it is easily damaged during spray drying which is usually used to produce infant formula powders. In this study, we showed that the extent of lysine loss can be controlled by adjusting the air inlet temperature and the air-to-liquid ratio. Depending on the spray drying conditions, 10.4±2.9% lysine loss down to no lysine loss was determined after spray drying in laboratory scale and in pilot scale. A main impact on lysine loss could be attributed to the particle residence time which was shown to be longer for the short-form, pilot-scale spray dryer than for the tall-form, laboratory-scale spray dryer. Median particle residence time was 6 s in the laboratory scale dryer and 17 s in the pilot scale dryer. The air-to-liquid ratio of the spray dryer proved to be a good parameter to compare different types of spray dryers. The extent of lysine loss during storage of the spray dried powders was independent of the extent of lysine loss during spray drying. Lysine loss during storage can be reduced by low storage temperatures and low water contents of the powder. Coupling kinetics of lysine loss that take into account the physical state of lactose, i.e., glassy, rubbery, or crystalline, with the processing conditions and particle residence time during spray drying was shown to be a promising tool to improve the nutritional quality of spray dried infant formula.