Milk protein concentrate (MPC) powders are widely used dairy ingredients in a variety of food product formulations to improve the nutritional, functional, and sensory properties. Flowability and morphological characteristics are affected by processing, storage, particle size, and composition of the powder. This study investigated the flowability and morphological characteristics of commercial MPC powders with protein concentrations of 70–90% (wt/wt) after storage for 12 wk at 25 and 40°C. Powder flow properties [basic flowability energy (BFE), flow rate index (FRI), and permeability] and shear properties (cohesion and flow function) were measured using the Freeman Technology FT4 rheometer (FT4, Freeman Technologies, UK). After 12 wk of storage at 40°C, the BFE values significantly increased (P < 0.05) from 512 to 722 mJ with the increase in protein content from 70 to 90% (wt/wt). FRI was significantly higher (P < 0.05) for samples with high protein content (90%). Dynamic flow tests indicated that MPC powders with high protein content displayed higher permeability. Shear tests confirmed that the samples stored at 25°C were relatively more flowable than samples stored at 40°C. Also, the higher protein content samples showed poor shear flow behavior compared with low protein samples. The results indicated that MPC powders stored at 25°C had lesser cohesiveness and better flow characteristics than MPC powders stored at 40°C. The MPC powders showed distinctly different flow properties due to their difference in intrinsic physical and chemical composition. The circle equivalent diameter and elongation of MPC powders increased as protein content and storage temperature increased, whereas convexity decreased as protein content and storage temperature increased. The flow, shear, and morphological characterization can help us understand the behavior of MPC powders with different protein contents during storage and will be useful in the process design of handling, processing, and storage.