This study investigated the impact of dynamic high-pressure (DHP) treatment on the ability of whey protein isolate (WPI) to form associative complexes with pectin and to form aggregate particles after their subsequent heat treatment. Light scattering showed that DHP treatments disrupted preexisting WPI aggregates and assembled pectin chains. Complexes formed from WPI/pectin mixtures at pH 4.5 were an order of magnitude smaller when formed after DHP treatment, regardless of the degree of esterification. WPI/pectin complexes formed after DHP treatment were more stable against subsequent pH neutralization than complexes formed without DHP treatment, and WPI/high-methoxyl pectin (HMP) complexes had greater stability than WPI/low-methoxyl pectin (LMP) complexes. WPI/pectin particles prepared by thermal treatment of complexes at pH 4.5 were also smaller when prepared after DHP treatment. WPI/HMP particles were stable to subsequent pH neutralization, while WPI/LMP particles became larger after neutralization.