The control of storage as any other manufacturing steps of dairy powders is essential to preserve protein functional properties. This study aimed to determine the effects of different storage conditions on both protein denaturation and protein lactosylation in whey protein isolate (WPI) powder, and also on heat-induced aggregation. Two different storage temperature conditions (20 and 40 °C) were studied over 15 months. Our results showed that protein lactosylation progressively increased in WPI powders over 15 months at 20 °C, but heat-induced aggregation properties did not significantly differ from non-aged WPI. On the other hand, powders presented a high level of denaturation and aggregation at 40 °C from the first 2 weeks of storage, involving first protein lactosylation and then aggregation in the dry state. This was correlated with an increasing Browning Index from 15 days of storage. These changes occurred with a decrease in aggregate size after heat treatment at 5.8 ≤ pH ≤ 6.6 and modification of heat-induced aggregate shapes.