Recently, many elderly people in Korea have been consuming protein-enriched milk powders for dietary supplementation in sarcopenia. In general, protein powders are manufactured using a spray dryer, and their fine particles result in poor instant properties. Fluidized bed agglomeration (FBA) is an effective method for improving the physical properties of protein powders via particle granulation, such as flowability and wettability. Therefore, the effects of FBA on the rheological and physical properties of isolated soy protein (ISP)-enriched skim milk powder (SMP) were investigated in this study. The size of ISP-enriched SMP particles was significantly increased by FBA, leading to changes in the Carr index and Hausner ratio from fair flowability and intermediate cohesiveness to good flowability and low cohesiveness, respectively. The wettability of the granulated particles was also improved by FBA, and they exhibited a shorter wetting time below 10 s. However, a slight color change was observed after the FBA process. These findings contribute to the production of protein-enriched food powders with improved properties.