The impact of different drying techniques and storage conditions on the formation of carboxymethyl lysine (CML) as an advanced glycation end product (AGE) was investigated in various pilot-scale produced skim milk powders (SMP). CML, an indicator of advanced stages of the Maillard reaction, was analyzed by isotope dilution ESI-LC-MS/MS after drying and at intervals during storage for 200 days. The aim of this study is to increase the awareness that the development of AGEs can be hindered by controlled storage, which is mostly neglected at the domestic level by the consumers. Pilot-scale freeze-dryer, spray-dryer, and drumdryer were utilized for manufacturing SMPs. The storage was designed in such a way that it simulated how an average consumer keeps the dried products at home, specifically after opening the packages and how the products may be exposed to unfavorable conditions. To do so, four storage conditions including two temperatures (20°C, 30°C) and two relative humidities RH (33%, 52%) were studied and CML formation was monitored using LC-MS/MS. Our results show that the spray-dried samples developed two times higher CML after 200 days, compared to the freeze-dried samples, and this value was 1.6 times for the drum-dried samples. Storage at 52% RH developed 9.8-10 times more CML in the samples, in comparison with 33% RH, at the same storage temperature (P < 0.05). Our findings demonstrate that AGEs, molecules suspected to be involved in risks factors for auto-immune diseases, may be formed during storage of SMPs after opening the packages by the consumers.