We report on the structure of whey protein aggregates formed by a short heating coupled to shear at high temperatures (80-120) and neutral pH in scale-up processing conditions, using gel filtration chromatography, light scattering, small angle neutron scattering, and cryogenic transmission electron microscopy. The results are interpreted in terms of coexistence of residual non-aggregated proteins and aggregates. The characteristics of aggregates such as the size, the aggregation number and the shape evidence two different morphologies. Whereas aggregates formed at 80 °C show a selfsimilar structure down to a length scale of the monomer with a fractal dimension typical for reaction limited cluster aggregation (D~2.2), aggregates formed at higher temperature show a spherical morphology, with the structure from small angle neutron scattering data best modelled with the form factor of a polydisperse sphere. We compare the structure of these aggregates to that of aggregates formed in quiescent conditions at lab scale. The structure transition is interpreted in terms of a non-trivial interplay between three perturbation factors: interparticle interaction, temperature and shear.