Pulse Spray Drying (PSD) has potential as a sustainable means of skimmed milk powder (SMP) production. In this study, powders were obtained from PSD using different drying outlet temperatures (70, 80, 90 and 100 °C), and their characteristics were compared to those of traditional Spray Drying (SD). Native whey proteins were well preserved and Solubility Indexes were over 98% in all cases, despite powders obtained by PSD displaying lower solubility than the SD ones. No visual difference was observable in the powders (ΔE < 2); however, PSD powders were found to be yellower with a higher Browning Index. The drying technology did not have a significant effect on powder moisture content and bulk density. Particle size distribution and scanning electron microscopy images confirmed the presence of fine particles (<10 μm) in all samples that might have provided poor flowability and wetting behavior (overall Carr Index and Hausner ratio were 33.86 ± 3.25% and 1.52 ± 0.07, respectively). Higher amounts of agglomerated particles were found at low temperatures in the products processed with both technologies, but PSD samples showed a narrower particle size distribution and hollow particles with more wrinkles on the surface (probably due to the fast evaporation rate in PSD). Overall, PSD provided SMP with comparable physicochemical characteristics to SD and, once optimized at the industrial level, could offer significant advantages in terms of thermal efficiency without significant modification of the final product quality.