The formation of whey protein aggregates, often termed soluble aggregates, with specific physicochemical properties has been shown to result in improved functionality in gels, foams, emulsions, encapsulation, films and coatings. This work evaluated the potential of whey protein soluble aggregates to improve thermal stability in the presence of salts and determine the mechanism of improved thermal stability. Solutions of whey protein isolate (WPI) or β-lactoglobulin (β-lg) (7% w/w, pH 6.8) were heated for 10 min at 90 °C to form soluble aggregates. Native proteins and soluble aggregates were diluted to 3% w/w in solutions containing 0–108 mM NaCl and thermally treated (90 °C, 5 min). Turbidity, solubility, and viscosity were evaluated, in addition to ζ-potential and S o (surface hydrophobicity). Size exclusion chromatography coupled with multi-angle laser light scattering (SEC-MALLS) and dynamic light scattering were used to determine aggregate size and transmission electron microscopy (TEM) was used to evaluate aggregate shape. Use of soluble aggregates improved thermal stability due to their altered aggregate shape and higher charge, and resulted in final aggregates that were smaller and less dense, leading to reduced viscosity and turbidity, and increased solubility compared to native proteins. It is concluded that soluble aggregates formed under the appropriate conditions to produce the desirable physicochemical properties can be used to improve whey protein thermal stability with a possible application in beverages.