Thermal treatment to form functional, soluble whey protein aggregates often generates undesired off-flavours. The aim of the present study was to generate soluble aggregates of whey protein isolates (WPI) at lower temperature than traditionally used by introducing partial hydrolysis of WPI prior to thermal treatment. WPI was partially hydrolyzed either by Bacillus licheniformis protease (BLP) or by a trypsin type protease (TP) at pH 7.0 and 65 °C for 1–10 min prior to thermal treatment at 80 °C for 5–10 min to generate soluble protein aggregates. Partial hydrolysis by BLP and TP induced structural changes and exposure of free thiol groups, but no change of surface hydrophobicity of WPI. After incubation with BLP or TP and thermal treatment, the yield of protein aggregates was 36–48%, which was similar to the reference sample obtained by thermal treatment at 90 °C for 10 min. In addition to non-covalent interactions, disulfide bonds also contributed to the association of protein aggregates. The soluble protein aggregates obtained by BLP partial hydrolysis and thermal treatment, had particle size range of 10–100 nm in radius which was in the same range as observed for the reference sample; and samples obtained by TP treatment had a particle size range of 7–50 nm in radius. However, aggregates obtained by BLP or TP and thermal treatment were not UHT (140 °C/5 s) stable.