Whey protein consumption has been linked to several health benefits including increased satiety and metabolic regulation; therefore, there is interest in increased consumption of foods rich in whey proteins. Meal replacement beverages and sports drinks are categories of foods that contain whey proteins. However, low thermal stability—especially near the protein isoelectric point (pI)—limits the pH range and protein concentrations at which beverages can be formulated. Studies have shown that at a narrow pH range close to the pI, whey proteins and pectin self assemble into soluble complexes (SCs) that have improved colloidal stability. Our objectives were to 1) determine the conditions required to form stable whey protein-pectin SCs, 2) characterize physical properties of the SCs, and 3) evaluate the effect of SCs on bulk rheological properties. Soluble complexes were formed at various protein concentrations (1, 4, 5 and 6% wt/wt) with a constant protein to pectin ratio of 8:1 by adjusting the pH from 7 to 5. After complexation, particles were stabilized by heating at 85°C for 25 min. The properties of unheated and heat-set SCs were characterized via intrinsic viscosity, particle size distribution, and rheological analysis. Laser diffraction particle size analysis revealed that heating shifted sizes toward a monomodal distribution with mean diameter of ~100 nm for all protein concentrations. Heat-stabilization significantly reduced intrinsic viscosity of SCs from 93.6 mL/g to 79.5 mL/g (P < 0.05), suggesting conformational changes that favor a smaller hydrodynamic size. Decreased viscosity of heat-set SCs was consistent with intrinsic viscosity and particle size results. Increasing protein concentration had very little effect on size of heat-set SCs, suggesting applications in beverages where a high protein concentration is desired. Heat-set SCs remained as 100 nm particles and did not aggregate over the pH range of 3–6. Moreover, they remained stable in this pH range after thermal processing. These results indicate that whey protein-pectin SCs can be heat-set into 100 nm particles with enhanced colloidal stability for applications in beverages.